While this guide includes a perfect build, it's more about finding your own perfect build. While some consideration is given to those without the DLC, this guide is geared towards the expectation that you have all of the DLC. I wrote this guide for myself, so I could understand what I want to do. Now that it's done, I published it here for others to make use of.
IMPORTANT NOTE: Make sure you have fully patched Fallout 3! Here is a guide on how to do that and more.
Slightly less important note: Make sure that none of your stats are being buffed (put away your Lucky 8-Ball, specifically) when you take the Almost Perfect perk and do not pick up any stat bobbleheads before you take the perk. The exception is if you have a stat (specifically IN) that is already at 9.
Warning: While I try to avoid it, it's inevitable that some spoilers will be talked about or mentioned here.
Vault 101
In Vault 101, you have to choose your stats and tag three skills for a +15 bonus to each. Below are my recommendations followed by explanations on why.
Preferred Perfect Build Example:
ST 5
PE 6
EN 6 (alt: 7)
CH 1
IN 9 (alt: 8)
AG 7
LK 6
Tag: Explosives, Repair, Speech (+15 bonus)
Note: This was a flawed example of a generic build to use as a starting point. I made the New Preferred Perfect Build to try to offer a more meaningful starting point to customize your build.
Another Example:
ST 1
PE 6
EN 6 (alt: 7)
CH 5
IN 9 (alt: 8)
AG 7
LK 6
Tag: Melee Weapons, Science, Lockpick (+15 bonus)
Note: This build was meant to show off that ST and CH are both considered the least useful stats and it doesn't really matter which one you dump leftover points into. ST is useful for carry weight and melee, which help you a lot more in early levels than CH but CH can be useful for people wanting a slightly easier time with Speech checks.
New Preferred Perfect Build Example:
ST 5
PE 5 (+1 Ant Sight)
EN 7
CH 1
IN 9
AG 7
LK 5 (+1 Lucky 8-Ball)
Tag: Explosives, Repair, Speech
Alt Tag: Small Guns/Melee Weapons, Picklock, Speech
Note: This is a combination of the minimum stat requirements to pick any perk you want and have enough skill points from leveling up that you don't even have to pick Comprehension, if you really don't want it. It's meant as a starting line for finding your own build and has a leftover stat point.
Imperfect Build Example:
ST 4
PE 8 (+1 Ant Sight)
EN 5
CH 1
IN 9
AG 6
LK 7 (+1 Lucky 8-Ball)
Tag: Melee Weapons, Repair, Speech
Note: This example was aimed at a more practical example for people not trying to take the Almost Perfect perk.
An end game build by /u/TomaszPaw
A pure combat build by /u/watboschitt
SPECIAL Discussion
Most perks with stat requirements cap out at 6, with a few that require 7. PE, EN, IN, AG are the four stats that need to be at 7 for certain perks. The only perk requiring an AG of 7 is from the Broken Steel DLC. So, you'll probably want most stats at 6. It's worth mentioning that you can take up to 10 ranks of Intense Training to raise stat points but, unless you're going for a very specific build without Almost Perfect, it's generally not recommended. Stats themselves aren't terribly useful outside of their ability to unlock perks. Even IN isn't necessary, if you take Comprehension.
ST is the only stat that caps out at 5 in terms of perk prerequisites. Depending on your playstyle and mods, you might consider ST entirely useless. Personally, the carry weight alone is worth it. That said, unless you plan to do a melee build or struggle too much with ammo, you can leave it at 5. If you really don't care about carry weight, you can leave it at 1. It's worth noting that you can get +1 from the Ant Might quest perk.
PE is pretty good but the only perk requiring it to be 7 is Infiltrator. It's not too hard to just avoid breaking locks though, as long as you don't have a habit of trying to force locks. Perks requiring it are mostly crit based. The exception being Thief that requires it to be at 4. It's worth noting that you can get +1 from the Ant Sight quest perk.
EN is useful but the Solar Powered, Rad Tolerance and Rad Absorption perks are really lacking for such high requirements. The +2 ST will be mostly useless and the HP regen isn't terribly useful either. Rad Tolerance is slightly more useful but easily skipped. Rad Absorption is slightly more useful, and combined with Rad Tolerance, they do a great deal to negate the need for curing radiation poisoning but aren't as important by the time you hit level 30. That said, a build with Rad Tolerance, Rad Absorption and Rad Regeneration could prove interesting.
CH is fairly useless outside of persuading NPCs and better trade prices. It should either be set to 1, 4 (Child at Heart) or 6 (Animal Friend, Master Trader,) depending on what related perks you want. It's unlikely you will struggle to have enough caps.
IN is truly mandatory and should be at 8 or 9 from the start. If you get it at 9 by level 2, you can go to Rivet City at the start and pick up the bobblehead for a total of 10 from level 2 onward. While it's unnecessary for getting max skills, it does give a bit of leeway for the pursuit of it. There are two ways to reach 9 IN right out of Vault 101. The most obvious would be to set it to that right away, the other method would be to set it to 8 and take the Intense Training perk at level 2. There's no point discussing perks that require it, since no one interested in this guide would have it lower than 7. However, low IN builds are viable, since Comprehension alone can make up for it.
AG is useful and so is the Nerves of Steel perk, for regenerating AP. However, it loses significance, if you take Grim Reaper's Sprint. It would be rare to encounter a fight where both perks would be helpful but it does happen. So, AG will need to be 7, if you want Nerves of Steel and 6, if you don't. If you don't use VATS at all, this stat is a lot less meaningful.
LK adds to all skills (at +1 per 2 LK, rounded up) and to crit. Scrounger (LK 5) and Better Crits (PE 6, LK 6) are the only perks really worth mentioning. Mysterious Stranger isn't the best perk (though, I'm sure some would debate that) but it's interesting and impacts the dialog with Somah in the Mothership Zeta DLC. Don't forget that you can get +1 from the Lucky 8-Ball.
While stats aren't exactly useless, the primary goal with picking them is usually to make sure you can grab the perks you want. Ultimately, your perk choices and maxing your skills will have the biggest impact on how you play, outside of what gear you find.
S.P.E.C.I.A.L. Stats
Tagged Skills:
Explosives will help with a quest in Megaton, the first town you reach after leaving the vault. That said, you can use the Mentats found in the Overseer's office to accomplish the same thing.
Repair is very useful for keeping weapons in working condition, especially early on.
Speech will help with conversations.
Other considerations:
Small Guns will definitely help with fighting, since it's the most common type of gun you'll find.
Melee Weapons will also help a great deal early on, especially with how limited ammo is.
Science can help with hacking.
Lockpick can help with lockpicking.
While the rest are useful, they aren't usually that helpful at the start.
Reference: Skills
Skill Points: The Math
Base: 2 + (Stat x 2) + RoundUp(Luck/2)
Level up: 10 + IN per level (not retroactive)
Max Base Skill: 2 + (10 (Almost Perfect + stat bobblehead) x 2) + (10 (LK) / 2) + 10 (Skill bobblehead) = 37
Covert Ops - +3 to Science, Small Guns and Lockpick (3 x 3) = 9
3 Tagged Skills: 3 x 15 = 45
45 + 9 = 54 tag adjustment
Skills
Barter (CH * 2) + 2 + (LK / 2)
Big Guns (EN * 2) + 2 + (LK / 2)
Energy Weapons (PE * 2) + 2 + (LK / 2)
Explosives (PE * 2) + 2 + (LK / 2)
Lockpick (PE * 2) + 2 + (LK / 2)
Medicine (IN * 2) + 2 + (LK / 2)
Melee Weapons (ST * 2) + 2 + (LK / 2)
Repair (IN * 2) + 2 + (LK / 2)
Science (IN * 2) + 2 + (LK / 2)
Small Guns (AG * 2) + 2 + (LK / 2)
Sneak (AG * 2) + 2 + (LK / 2)
Speech (CH * 2) + 2 + (LK / 2)
Unarmed (EN * 2) + 2 + (LK / 2)
In the preferred example, this would be the results:
ST: 2 + (5 x 2) + 6/2 = 15
PE: 2 + (6 x 2) + 6/2 = 17
EN 2 + (6 x 2) + 6/2 = 17 (alt: 2 + (7 x 2) + 6/2 = 19)
CH 2 + (1 x 2) + 6/2 = 7
IN 2 + (9 x 2) + 6/2 = 23 (alt: 2 + (8 x 2) + 6/2 = 21)
AG 2 + (7 x 2) + 6/2 = 19
LK 2 + (6 x 2) + 6/2 = 17
Barter 2 + (1 x 2) + 6/2 = 7
Big Guns 2 + (6 x 2) + 6/2 = 17 (alt: 2 + (7 x 2) + 6/2 = 19)
Energy Weapons 2 + (6 x 2) + 6/2 = 17
Explosives 2 + (6 x 2) + 6/2 = 17
Lockpick 2 + (6 x 2) + 6/2 = 17
Medicine 2 + (9 x 2) + 6/2 = 23 (alt: 2 + (8 x 2) + 6/2 = 21)
Melee Weapons 2 + (5 x 2) + 6/2 = 15
Repair 2 + (9 x 2) + 6/2 = 23 (alt: 2 + (8 x 2) + 6/2 = 21)
Science 2 + (9 x 2) + 6/2 = 23 (alt: 2 + (8 x 2) + 6/2 = 21)
Small Guns 2 + (7 x 2) + 6/2 = 19
Sneak 2 + (7 x 2) + 6/2 = 19
Speech 2 + (1 x 2) + 6/2 = 7
Unarmed 2 + (6 x 2) + 6/2 = 17 (alt: 2 + (7 x 2) + 6/2 = 19)
(9 IN lvl 1) 221 subtotal
+54 tag adjustment
275 subtotal
+130 bobblehead adjustment
405 subtotal
+551 at level 30 (lvl 2-30)
956 subtotal
+28 Rivet City bobble head (lvl 3-30; 28 lvl x 1 IN)
984 subtotal
+130 Almost Perfect + SPECIAL bobbleheads at lvl 30 ((2 + (10 x 2) + (10 / 2)) x 13 = 351; 351 - 221 = 130)
1114 subtotal
+325 skill books
1439 subtotal
+325 Comprehension perk
1764 total
551 + 28 = 579 bonus level up points + 54 tag adjustment = 633 / 13 skills = 48 r9 per skill
37 (max base) + 48 (bonus) + 25 (skill books) = 110 total points per skill with 9 leftover
Unlimited Science and Big Guns skill book adjustment.
551 + 28 = 579 bonus level up points + 54 (-3 Science) tag adjustment = 630 / 11 skills = 57 r2 per skill
37 (max base) + 57 (bonus) + 25 (skill books) = 119 total points per skill with 5 leftover
119 + 25 (Comprehension) = 144 total points per skill with 2 leftover
(8 IN lvl 1) 219 subtotal
+54 tag adjustment
264 subtotal
+130 bobblehead adjustment
394 subtotal
+522 at level 30 (lvl 2-30; 29 lvl x (10 + 8 IN))
916 subtotal
+132 Almost Perfect + SPECIAL bobbleheads at lvl 30 ((2 + (10 x 2) + (10 / 2)) x 13 = 351; 351 - 219 = 132)
1048 subtotal
+325 skill books
1373 subtotal
+325 Comprehension perk
1698 total
522 bonus level up points + 54 tag adjustment = 576 / 13 skills = 44 r4 per skill
37 (max base) + 44 (bonus) + 25 (skill books) = 106 total points per skill with 4 points leftover
Unlimited Science and Big Guns skill book adjustment.
522 bonus level up points + 54 (-3 Science) tag adjustment = 573 / 11 skills = 52 r1 per skill
37 (max base) + 52 (bonus) + 25 (skill books) = 114 total points per skill with 1 leftover
114 + 25 (Comprehension) = 139 total points per skill with 4 leftover
A Min/Max build:
ST 4
PE 8 (+1 Ant Sight)=9
EN 6 (+1 Intense Training)=7
CH 1
IN 9
AG 5
LK 8 (+1 Lucky 8-ball)=9
ST: 2 + (4 x 2) + 9/2 = 15
PE: 2 + (9 x 2) + 9/2 = 25
EN 2 + (7 x 2) + 9/2 = 21
CH 2 + (1 x 2) + 9/2 = 9
IN 2 + (9 x 2) + 9/2 = 25
AG 2 + (5 x 2) + 9/2 = 17
LK 2 + (9 x 2) + 9/2 = 25
Barter 2 + (1 x 2) + 9/2 = 9
Big Guns 2 + (7 x 2) + 9/2 = 21
Energy Weapons 2 + (9 x 2) + 9/2 = 25
Explosives 2 + (9 x 2) + 9/2 = 25
Lockpick 2 + (9 x 2) + 9/2 = 25
Medicine 2 + (9 x 2) + 9/2 = 25
Melee Weapons 2 + (4 x 2) + 9/2 = 15
Repair 2 + (9 x 2) + 9/2 = 25
Science 2 + (9 x 2) + 9/2 = 25
Small Guns 2 + (5 x 2) + 9/2 = 17
Sneak 2 + (5 x 2) + 9/2 = 17
Speech 2 + (1 x 2) + 9/2 = 9
Unarmed 2 + (7 x 2) + 9/2 = 21
(lvl 1) 259 subtotal
+54 tag adjustment
313 subtotal
+130 bobblehead adjustment
443 subtotal
+551 at level 30 (lvl 2-30; 29 lvl x (10 + 9 IN))
994 subtotal
+28 Rivet City bobble head (lvl 3-30; 28 lvl x 1 IN)
1022 subtotal
+92 Almost Perfect + SPECIAL bobbleheads at lvl 30 ((2 + (10 x 2) + (10 / 2)) x 13 = 351; 351 - 259 = 92)
1114 subtotal
+325 skill books
1439 subtotal
+325 Comprehension perk
1764 total
551 + 28 = 579 bonus level up points + 54 tag adjustment = 633 / 13 skills = 48 r9 per skill
37 (max base) + 48 (bonus) + 25 (skill books) = 110 total points per skill with 9 leftover
Unlimited Science and Big Guns skill book adjustment.
551 + 28 = 579 bonus level up points + 54 (-3 Science) tag adjustment = 630 / 11 skills = 57 r2 per skill
37 (max base) + 57 (bonus) + 25 (skill books) = 119 total points per skill with 5 leftover
119 + 25 (Comprehension) = 144 total points per skill with 2 leftover
Skill Points: Explanation
So, we start with the formula on the previously linked Skills page. Know that there are 13 skills requiring 100 points each, meaning we need a total of 1300 skill points to hit max. Temporary points from most clothing (the exception being the Lucky 8-ball) and drugs do not count.
Don't forget about the 3 tagged skills for a total of +45 points.
There are bobbleheads that give +10 to each skill. They will not raise a skill above the cap of 100, so grab them when you see them. We'll call them the bobblehead adjustment for a total of 130 points.
There's also the Comprehension perk and 25 of each type of skill book. This gives a theoretical (assuming you get the perk and then collect/read all of the skill books) +50 to all skills for a total of 650 points. You can take your skills higher than 100 by maxing them before reading all of the books.
It's worth noting that the Science and Big Guns books have a single source each that respawns about every 72-73 in-game hours. There's also at least one item that grants a bonus to skills.
I don't recommend it and did not count it in the math but the Educated perk would probably be helpful to anyone without the DLC. Since the level cap is 20 without the DLC, you'll only get about 48 skill points from it but that's still better than most perks, aside from Comprehension.
Finally, you get 10 + IN per level (not retroactive) for each level up.
As you can see in the math section, if you want to min/max skill points, you would do best to have an odd number of LK and to give more points to PE and IN while giving less to ST. Of course, it's not necessary to min/max this much to reach max skill points. As you can see from the totals, it's not that difficult to hit the limit. In fact, taking Comprehension by itself at least guarantees that you have the opportunity to max all skills. That said, you could with the right build and by playing carefully, you can even skip Comprehension and still max your skills.
After adjusting for the fact you can get unlimited Science and Big Guns skill books (they both have a single source that respawns every 72 in game hours,) you can see that not only can you skip Comprehension, even Almost Perfect isn't necessary for maxing skills.
While the skill page explains that you can max your skills simply by getting them all to 40, thanks to the Comprehension perk and skill books, it doesn't mention that some skill books can be missed either due to having to obtain them at a specific time or not taking certain (Lawbringer and Contract Killer) perks.
The New Preferred Build example takes into account bonuses that the old one doesn't. The Imperfect Build is an experiment in allowing you to take any perk you want, still have a really good chance of maxing your skills and being able to skip the Almost Perfect perk entirely. The expectation with the Imperfect Build is that you'll grab all of the bobbleheads, Ant Sight and the Lucky 8-Ball as soon as you leave 101.
I linked to a couple of builds from the comments that are well refined with a specific goal in mind. Neither of them use the Almost Perfect perk but both are very effective builds.
Again, the purpose of this guide is to find what is perfect for you. So, having build samples and explanations in the comments is great.
Further reading:
Perks
Skill Books
Quests
Perks
Note: Optional perks are listed as such to either be used in that perk slot or later levels marked as a Free Slot. I placed my personal choices as recommendations but feel free to pick something else. My recommendations trend towards being generalized and completionist.
Level 2 - Swift Learner (IN 4) - +10% XP whenever XP is earned
Optional: Intense Training - +1 to any SPECIAL stat
Level 3 - Lady Killer/Black Widow - +10% damage against opposite sex, more useful if your character is a girl but still this perk isn't too bad.
Level 4 - Comprehension (IN 4) - +1 additional skill point whenever a skill book is read
Optional: Educated (IN 4) - +3 skill points per level (only take at lvl 4; should result in 78 skill points)
Optional: Iron Fist - +5 points of Unarmed Damage
Optional: Child at Heart - Unlocks many unique dialogue options with children
Level 5 - Free Slot (Recommend: Entomologist - +50% damage to insects)
Level 6 - Toughness (EN 5) - +10% DR permanently
Optional: Bloody Mess - +5% overall damage, more violent death animations
Optional: Gunslinger - +25% accuracy in V.A.T.S. with one-handed weapons
Optional: Demolition Expert (Explosives 50) - +20% damage with explosives
Optional: Fortune Finder (LK 5) - Considerably more bottle caps will be found in containers
Level 7 - Free Slot (Recommend: Bloody Mess - +5% overall damage, more violent death animations)
Level 8 - Free Slot (Recommend: Strong Back (EN 5) - +50 Carry Weight)
Optional: Strong Back (EN 5) - +50 Carry Weight
Optional: Rad Resistance (EN 5) - +25% Radiation Resistance permanently
Optional: Commando - +25% accuracy in V.A.T.S. with two-handed weapons
Optional: Scrounger - Considerably more ammunition in containers
Level 9 - Free Slot (Recommend: Scrounger - Considerably more ammunition in containers)
Level 10 - Finesse - +5% Critical Chance
Optional: Mysterious Stranger (LK 6) - Chance that the Stranger will finish off a target in V.A.T.S. and extra dialog in Mothership Zeta DLC
Optional: Animal Friend (CH 6) - Hostile animals become friendly (one rank), and come to your aid except against other animals (two ranks).
Optional: Nerd Rage! (IN 5, Science 50) - +50% DR and Strength increased to 10 whenever health is 20% or lower
Level 11 - Free Slot (Recommend: Rad Resistance (EN 5) - +25% Radiation Resistance permanently)
Level 12 - Free Slot (Recommend: Robotics Expert (Science 50) - +25% damage to robots, can shut down robots by sneaking up on them)
Optional: Robotics Expert (Science 50) - +25% damage to robots, can shut down robots by sneaking up on them
Optional: Life Giver (EN 6) - +30 Hit Points
Optional: Sniper (PE 6, AG 6) - +25% to hit the target's head in V.A.T.S.
Optional: Silent Running (AG 6, Sneak 50) - +10 Sneak, foot speed and armor weight no longer affect sneaking
Optional: Fast Metabolism - +20% Hit Points restored with stimpaks
Optional: Pyromaniac (Explosives 60) - +50% damage with fire-based weapons
Optional: Cannibal - Can eat corpses to restore 25 points of health and lose 1 Karma
Level 13 - Free Slot (Recommend: Silent Running (AG 6, Sneak 50) - +10 Sneak, foot speed and armor weight no longer affect sneaking)
Level 14 - Adamantium Skeleton - Damage taken by limbs reduced by 50%
Optional: Lawbringer - Can sell fingers to Sonora Cruz
Optional: Contract Killer - Can sell ears to Daniel Littlehorn
Optional: Chemist (Medicine 60) - Chems last twice as long
Optional: Light Step (PE 6, AG 6) - Floor traps or mines will not be set off
Optional: Master Trader (CH 6, Barter 60) - All items cost 25% less
Level 15 - Cyborg (Medicine 60, Science 60) - +10 Energy Weapons, +10% to Radiation Resistance, Poison Resistance and Damage Resistance
Level 16 - Action Boy/Action Girl (AG 6) - +25 Action Points
Optional: Chem Resistant (Medicine 60) - Half as likely to get addicted
Level 17 - Better Criticals (PE 6, LK 6) - +50% damage with critical hits
Level 18 - Free Slot (Recommend: Contract Killer - Can sell ears to Daniel Littlehorn)
Optional: Concentrated Fire (Energy Weapons 60, Small Guns 60) - +5% accuracy in V.A.T.S. with every attack queued
Optional: Paralyzing Palm (Unarmed 70) - 30% to paralyze an enemy for 30 seconds with an unarmed attack in V.A.T.S.
Level 19 - Free Slot (Recommend: Lawbringer - Can sell fingers to Sonora Cruz)
Level 20 - Grim Reaper's Sprint - A kill in V.A.T.S. restores all your AP immediately
Optional: Ninja (Melee Weapons 80, Sneak 80) - +15% critical chance with melee and unarmed weapons, +25% damage with sneak attack criticals (+15% crit is bugged unless patched)
Optional: Explorer - All locations are marked on your map
Optional: Solar Powered (EN 7) - +2 Strength and +1 HP every 10 seconds while outside, from 6:00 a.m. to 6:00 p.m.
DLC: Those without the DLC will cap out here.
Level 21 - Free Slot (Recommend: Explorer - All locations are marked on your map)
Level 22 - Free Slot (Recommend: Quantum Chemist (Science 70) - Every 10 Nuka-Colas you acquire are automatically converted into a Nuka-Cola Quantum)
Optional: Quantum Chemist (Science 70) - Every 10 Nuka-Colas you acquire are automatically converted into a Nuka-Cola Quantum
Optional: Puppies! - If Dogmeat dies, a puppy will spawn outside of Vault 101
Optional: Deep Sleep - Sleeping in any bed gives the Well Rested effect, which increases your XP by 10%, for 8 hours. (only take at lvl 22)
Level 23 - Free Slot (Recommend: Mysterious Stranger (LK 6) - Chance that the Stranger will finish off a target in V.A.T.S. and extra dialog in Mothership Zeta DLC)
Level 24 - Free Slot (Recommend: Ninja (Melee Weapons 80, Sneak 80) - +15% critical chance with melee and unarmed weapons, +25% damage with sneak attack criticals (+15% crit is bugged unless patched))
Optional: No Weaknesses - All SPECIAL stats lower than 5 become 5
Level 25 - Free Slot (Recommend: Light Step (PE 6, AG 6) - Floor traps or mines will not be set off)
Level 26 - Free Slot (Recommend: Nerves of Steel (AG 7) - +1 AP every 10 seconds)
Optional: Nerves of Steel (AG 7) - +1 AP every 10 seconds
Optional: Rad Tolerance (EN 7) - No effects from minor radiation poisoning (still gives alert)
Optional: Warmonger (IN 7) - All schematics are added at V3
Level 27 - Free Slot (Recommend: Life Giver (EN 6) - +30 Hit Points)
Level 28 - Free Slot (Recommend: Rad Absorption (EN 7) - -1 Rad every 20 seconds)
Optional: Party Girl/Party Boy - No chance for alcohol addiction
Optional: Rad Absorption (EN 7) - -1 Rad every 20 seconds
Level 29 - Free Slot (Recommend: Child at Heart - Unlocks many unique dialogue options with children)
Level 30 - Almost Perfect - All SPECIAL stats are raised to 9
Optional: Nuclear Anomaly - Whenever your health is reduced to 20 or less, you will erupt into a devastating nuclear explosion
Perk Discussion
Note: Most perks that add skill points are skippable, unless you are playing without the Broken Steel DLC. Again, my advice is generally aimed at those with all the DLC.
General Perks
LVL 2 - 3
Black Widow/Lady Killer - +10% damage to the opposite sex, and unique dialogue options with certain characters
Daddy's Boy/Daddy's Girl (IN 4) - +5 Science, +5 Medicine
Gun Nut (IN 4, AG 4) - +5 Small Guns, +5 Repair
Little Leaguer (ST 4) - +5 Melee Weapons, +5 Explosives
Thief (PE 4, AG 4) - +5 Lockpick, +5 Sneak
Swift Learner (IN 4) - +10% XP whenever XP is earned (only take at lvl 2)
Intense Training - +1 to any SPECIAL stat
Unless you are strugging to max your skills, the only ones worth talking about are Black Widow/Lady Killer, Swift Learner and Intense Training. Black Widow/Lady Killer is a no brainer as the first choice. This leaves either Swift Learner or Intense Training. Unless you have a SPECIAL need to increase a stat by one point, Swift Learner wins by default, simply for being able to level up faster. Daddy's Boy/Daddy's Girl, Gun Nut, Little Leaguer and Thief are all skippable.
LVL 4 - 5
Child at Heart (CH 4) - Unlocks many unique dialogue options with children
Comprehension (IN 4) - +2 skill points from books
Educated (IN 4) - +3 skill points per level (only take at lvl 4)
Entomologist (IN 4, Science 40) - +50% damage to insects
Scoundrel (CH 4) - +5 Speech, +5 Barter
Iron Fist (ST 4) - +5 points of Unarmed Damage
Comprehension is the true must-have here, since we're talking about basically +25 to all skills from books. Educated is really pointless, compared to comprehension, but might be useful for someone without the DLC. Entomologist is useful against bugs. Iron Fist is great, if you are doing an Unarmed build. If you really want to do it for the lore, you can pick Child at Heart. Scoundrel is skippable.
LVL 6 - 7
Bloody Mess - +5% overall damage, more violent death animations
Lead Belly (EN 5) - -50% radiation taken whenever drinking from a water source
Toughness (EN 5) - +10% DR permanently
Fortune Finder (LK 5) - Considerably more bottle caps will be found in containers
Gunslinger - +25% accuracy in V.A.T.S. with one-handed weapons
Demolition Expert (Explosives 50) - +20% damage with explosives
The first time we need some real debate. Bloody Mess is a straight damage bonus and cool looking, so it shouldn't be ignored. Leady Belly is skippable, unless you are in the habit of needing to drink from contaminated water. Toughness is a must-have for any build. Fortune Finder is convenient but not necessary. Gunslinger is pretty much a must-have for one-handed gun builds. Demolition Expert is pretty great for any explosives (grenades and mines only) heavy build.
LVL 8 - 9
Commando - +25% accuracy in V.A.T.S. with two-handed weapons
Rad Resistance (EN 5) - +25% Radiation Resistance permanently
Scrounger - Considerably more ammunition in containers
Size Matters (LK 5) - +15 Big Guns
Strong Back (EN 5) - +50 Carry Weight
Impartial Mediation (CH 5) - +30 Speech when you have neutral Karma
Commando is the two-handed version of Gunslinger. Rad Resistence is the must-have from this group. Scrounger is actually useful (unless modded otherwise) due to how rare ammo is. Strong Back is a favorite of loot hoarders, like me. Size Matters is skippable. Unless you want to deal with the headache of trying to maintain neutral Karma, skip Impartial Mediation.
LVL 10 - 11
Animal Friend (CH 6) - Hostile animals become friendly (one rank), and come to your aid except against other animals (two ranks).
Finesse - +5% Critical Chance
Mister Sandman (Sneak 60) - Can instantly kill a sleeping non-player character and earns bonus XP
Mysterious Stranger (LK 6) - Chance that the Stranger will finish off a target in V.A.T.S. and extra dialog in Mothership Zeta DLC
Nerd Rage! (IN 5, Science 50) - +50% DR and Strength increased to 10 whenever health is 20% or lower
Night Person - +2 Intelligence and +2 Perception between 6:00 p.m. and 6:00 a.m.
Here and Now - You instantly level up again
Animal Friend is useful but not really worth it. Finesse is the closest to a must-have in this group. Mysterious Stranger is interesting but not incredibly useful. Mister Sandman, Nerd Rage!, Night Person and Here and Now are skippable. I'll note that Here and Now is tempting but a waste, since it's not that hard to gain a level, while it hurts my soul that Night Person is useless. Nerd Rage! is technically useful but only when you're already in a bad spot.
LVL 12 - 13
Pyromaniac (Explosives 60) - +50% damage with fire-based weapons
Cannibal - Can eat corpses to restore 25 points of health and lose 1 Karma
Life Giver (EN 6) - +30 Hit Points
Robotics Expert (Science 50) - +25% damage to robots, can shut down robots by sneaking up on them
Sniper (PE 6, AG 6) - +25% to hit the target's head in V.A.T.S.
Silent Running (AG 6, Sneak 50) - +10 Sneak, foot speed and armor weight no longer affect sneaking
Fast Metabolism - +20% Hit Points restored with stimpaks
Pyromaniac is really lacking, since it only boosts initial damage. Cannibal can be useful, as an intentional way to lower Karma. Life Giver is useful on all but the lowest difficulties. Robotics Expert is quite nice, especially for stealth builds. Sniper is useful for headshots, obviously. Silent Running is another that's great for stealth builds. Fast Metabolism boosts stimpaks.
LVL 14 - 15
Lawbringer - Can sell fingers to Sonora Cruz
Chemist (Medicine 60) - Chems last twice as long
Contract Killer - Can sell ears to Daniel Littlehorn
Cyborg (Medicine 60, Science 60) - +10 Energy Weapons, +10% to Radiation Resistance, Poison Resistance and Damage Resistance
Light Step (PE 6, AG 6) - Floor traps or mines will not be set off
Master Trader (CH 6, Barter 60) - All items cost 25% less
Adamantium Skeleton - Damage taken by limbs reduced by 50%
We're suddenly being spoilt for choice here. Lawbringer is a must-have for completionists and the same goes for Contract Killer. Chemist is useful but not strictly necessary. Cyborg is a must-have due to the resistances. Light Step is incredibly useful to anyone that is bad at avoiding traps but skippable for everyone else. Master Trader is convenient but skippable. Adamantium Skeleton is the true must-have in this group.
LVL 16 - 17
Tag! - Fourth "tag" skill: +15 points to that skill
Better Criticals (PE 6, LK 6) - +50% damage with critical hits
Action Boy/Action Girl (AG 6) - +25 Action Points
Chem Resistant (Medicine 60) - Half as likely to get addicted
Better Criticals is the first must-have and Action Boy/Girl is the second. Chem Resistant is convenient but not necessary. Tag! is skippable.
LVL 18 - 19
Infiltrator (PE 7, Lockpick 70) - Can pick a broken lock with one more bobby pin
Computer Whiz (IN 7, Science 70) - Can hack a locked down terminal with four more chances
Concentrated Fire (Energy Weapons 60, Small Guns 60) - +5% accuracy in V.A.T.S. with every attack queued
Paralyzing Palm (Unarmed 70) - 30% to paralyze an enemy for 30 seconds with an unarmed attack in V.A.T.S.
Infiltrator and Computer Whiz sound useful but really aren't, since they only help you overcome truly stupid and avoidable mistakes like forcing a lock (and failing) or getting locked out of a terminal. Concentrated Fire is good for any gun build. Paralyzing Palm is good for unarmed builds.
LVL 20 - 21
Solar Powered (EN 7) - +2 Strength and +1 HP every 10 seconds while outside, from 6:00 a.m. to 6:00 p.m.
Ninja (Melee Weapons 80, Sneak 80) - +15% critical chance with melee and unarmed weapons, +25% damage with sneak attack criticals (+15% crit is bugged unless patched)
Grim Reaper's Sprint - A kill in V.A.T.S. restores all your AP immediately
Explorer - All locations are marked on your map
Solar Powered isn't really that useful. Ninja is great for melee and unarmed builds. Grim Reaper's Sprint is the true must-have of this group. Explorer is a very convenient QoL perk but not actually necessary.
DLC Perks
LVL 22 - 23
Deep Sleep - Sleeping in any bed gives the Well Rested effect, which increases your XP by 10%, for 8 hours. (only take at lvl 22)
Puppies! - If Dogmeat dies, a puppy will spawn outside of Vault 101
Quantum Chemist (Science 70) - Every 10 Nuka-Colas you acquire are automatically converted into a Nuka-Cola Quantum
Deep Sleep isn't really worth it. Puppies! is either the best perk or the worst one, depending on how often you let Dogmeat die. Quantum Chemist is a must-have for anyone in need of unlimited Nuka-Cola Quantum.
LVL 24 - 25
Devil's Highway (Karma higher than Very Evil) - Karma is instantly set to Very Evil
Escalator to Heaven (Karma lower than Very Good) - Karma is instantly set to Very Good
Karmic Rebalance (Karma not neutral) - Karma is instantly set to Neutral
No Weaknesses - All SPECIAL stats lower than 5 become 5
These are all skippable. There are ways to lower/raise karma without wasting a perk slot. No Weaknesses would only be useful under very specific circumstances where you absolutely need to raise a stat to 5 before level 30, since it's fully trumped by Almost Perfect.
LVL 26
Rad Tolerance (EN 7) - No effects from minor radiation poisoning (still gives alert)
Warmonger (IN 7) - All schematics are added at V3
Nerves of Steel (AG 7) - +1 AP every 10 seconds
The only truly useful one is Nerves of Steel and that can normally be skipped, if you took Grim Reaper's Sprint. The other two are skippable conveniences.
LVL 28
Party Girl/Party Boy - No chance for alcohol addiction
Rad Absorption (EN 7) - -1 Rad every 20 seconds
These are both skippable convenience perks and with Rad Absorption requiring 7 EN, it's only accessible to a build that was basically based around it from the start.
LVL 30
Nuclear Anomaly - Whenever your health is reduced to 20 or less, you will erupt into a devastating nuclear explosion
Almost Perfect - All SPECIAL stats are raised to 9
These are both useful but, if you're going for a perfect build, the choice was already made at the start.
Special Perks
Dream Crusher - Wasteland Survival Guide - Talk Moira Brown out of writing the Wasteland Survival Guide - Reduces an enemy's chance to critically hit you by 50%, 30% discount at Craterside Supply, and +30 points to Moira's Repair skill (54, 72% condition).
Hematophage - Blood Ties - Talk to Vance about learning the ways of a vampire - Blood packs heal 20 Hit Points instead of 1 point
Power Armor Training - Learned from Paladin Gunny in the Citadel or by completing Operation: Anchorage! - You're now able to wear any form of power armor.
DLC
Covert Ops - Operation: Anchorage - Gather all 10 Intel suitcases - +3 to Science, Small Guns and Lockpick
Auto Axpert - The Pitt - Unsafe Working Conditions - Collect 10 steel ingots in the steelyard - +25% more damage with the auto axe
Ghoul Ecology - Point Lookout - Plik's Safari - Read Plik's journal - +5 points of damage to all enemies (due to a glitch)
Xenotech Expert - Mothership Zeta - This Galaxy Ain't Big Enough... - Get a random number of enemies to spawn in shooting range. - +20% damage with alien weapons
Quest Perks
Ant Might - Complete Those! without eliminating the fire ant queen OR eliminating the queen and convincing Doctor Lesko it was better for mankind (speech check) - +1 ST and +25% Fire Resistance (Mutually exclusive with Ant Sight)
Ant Sight - Complete Those! without eliminating the fire ant queen OR eliminating the queen and convincing Doctor Lesko it was better for mankind (speech check) - +1 PE and +25% fire resistance (Mutually exclusive with Ant Might)
Barkskin - Quest: Oasis - Destroy Harold's heart - +5 DR permanently
Rad Regeneration - Help Moira Brown with the Wasteland Survival Guide by gaining 600 rads when she asks - With the Rad Regeneration perk, any crippled limbs will regenerate themselves when you have Advanced Rad Poisoning
Survival Expert (Junior Survivor/Survival Guru) - Help Moira Brown finish the Wasteland Survival Guide by completing the final chapter - Varies: You gain a +6% bonus to Poison Resistance and Radiation Resistance and either additional Crit %, additional DR, additional HP, or points to both Medicine and Science or Sneak and Speech.
Wired Reflexes - Quest: The Replicated Man - Side with Dr. Zimmer - +10% accuracy in V.A.T.S.
DLC
Booster Shot - The Pitt - Free Labor - Complete Free Labor - +10% Radiation Resistance
Pitt Fighter - The Pitt - Unsafe Working Conditions - Complete the Hole battles - +3% Radiation Resistance and +3% Damage Resistance
Punga Power! - Point Lookout - Walking with Spirits - Complete Walking with Spirits - -10 Rads from wild punga fruit and -15 Rads from refined punga fruit
Superior Defender - Point Lookout - The Local Flavor - Complete The Local Flavor - +5 points of damage and +10 DR when standing still
If you made it this far, thanks for reading. Feel free to ask questions or make your own suggestions. If I got anything flat out wrong, I'll try to correct it.
Update: /u/TomaszPaw pointed out to me how unarmed is actually quite useful later in the game and he lists an interesting build, if anyone wants to try that. He's not the only person to respond with their own build and that's great. I didn't actually ask for it but I was really hoping people would respond with their own builds and explain why they like them and that's exactly what I'm getting. I really appreciate everyone's responses and build advice.
4/27/24 Update: I found some mistakes in the math section and added some potential bonuses that I missed.
4/27/24 Update2: Added a couple more build samples, linked a couple from the comments and added some more detail to my explanations.
6/6/24 Update3: I added notes explaining the build examples and a few minor revisions related to stats discussion.
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