If you can, read it later. There are dozens of great services, like Pocket or Instapaper, that allows you to save texts, files and even entire web-pages to read them later, when you have finished your other tasks. They are great, since you can also have offline versions of site-pages and you can install them on tablets/smartphones. This should prevent you from forgetting B, which will be what you like to do/read, after finishing A.

Bookmarkers gonna bookmark. If you find a cool site, full of interesting articles and stuff, during your study sessions (Drummer World took many of my time last year), bookmark it and then close the tab. Later, when you are done with homework, you will enjoy all those cool things, without regretting about study/PC shutting down.

Going back from B to A. I really found myself great with PDF annotation tools, because they allow you to do everything you would do with physical notebooks. So, if you are forced to interrupt your PDF reading, you can make an annotation or add a bookmark and then you can close the PDF. Here you will find suggestions about this.

Search and destroy. If you are searching for files, avoid using file explorer. Instead, press the Home button and type in your file name. This will decrease the "windows-opening rate" and consequently will save your PC from burning.

Organise your day. I personally think that GTD is not the best habit of having things done, but To-Do lists/applications can still be useful. Personally, I would suggest you to use Todoist or Todo.txt. The former comes with applications and plugins for many platform (sadly, not Ubuntu, but fortunately you can install it on Firefox and Thunderbird) and will please you with a good design. However, most interesting features are locked, unless you pass on a Premium account. The latter is more "terminal-style", and I think you will prefer that, because you can set your own rules and macros for priority/check/ponies.

Be yourself. Don't force yourself into an habit which doesn't suit you.

I suffered the exact problem. Over the years, I've learned a couple methods/tools that helped. But in general, it's more of a habit/process issue than the lack of hardware.

I'll first talk about some tools:

• For browser tabs, I like 'one tab' or something like 'simple window saver' (for chrome). Just find a session managing extension that helps you quickly save/restore windows and tabs.
• For online articles that are not critical to the work but nice to read, use Pocket or Read it Later to clip it. Get them out of the way and read when you are on your bed. There are just too many information out there. Don't feel bad if you ignore some of them.
• Use a to-do or note app that supports file links (even Evernote). With local files that I need to queue for later use, this is a good way to manage them.

Now the habit and process: Here's a simplified version of your scenarios:

1. I need to do B to help I do A.

   it's fine. I'm guessing most of 500 tabs are not from this. But if you need to learn C or even D to do A, it means you are too far away from accomplishing A, you need to save A's info at somewhere and abandon it for now and make C as your primary task.

2. I want to do B after I finish A but afraid I'll forget

3. I wan to do B later which is unrelated to A.

   For case 2 & 3, write B on a to-do or note app. Don't start exploring B and leave 50 tabs open that you aren't gonna be able to finish soon (since you are still on A) before you finish A.

I believe you must've switched from tasks to tasks to reach 500 tabs. It's important to focus on one thing at a time without getting sidetracked. If you were trying to tackle a problem that's too big, then you need to break it down to smaller chunks and work on one after another. A good practice is to pick 3 important task for the day every morning, and then use Pomodoro (work for 25 min non-stop and rest for 5 min). Then you are forced to define a task that's accomplishable in the next 25 min, which prevents you from getting distracted.

Sometimes I have lots of ideas coming out or want to check out what's the best way of doing XXX. It really affected my productivity. Putting them on a to-do list (which takes 2 sec) and immediately focus back to the current task helped a lot. However, you'll need to remember to go back and review the to-do list, but that's another story (GTD).

To summarize, human brains have capacity limits like computers, 500 tabs is too much for anyone to process. If you can't finish something in less than 2 min and jump to the next one, there's no need to keep them out there. It only slows your computer down and make your mind occupied by too much stuff.

Hope this helps and good luck.

Use OneTab. It is a Chrome/Firefox extension.

It allows you to - with a single right click - move all your 500 tabs into a list that is then persistent. This is better than bookmarking them, especially if you only want to read them once and because bookmarking 500 items is a pain.

I also tend to "multitask" heavily on my Kubuntu Laptop, especially when working intensively on different projects as a college student. However I was pretty ok with it once I got a little bit organized. Additionally I have a heavy tendency to procrastination, so it is important as well for me to separate work from entertainment. I also work in 3, sometimes 4 different languages, so I use a lot of online dictionaries, and like to check websites in different languages in parallel.

Here are some things I do to deal with these habits, it's rather newbie stuff (I'm not an expert user nor a professional, and I use Kate mainly because I'm struggling with Vim & co.) but I hope it helps answering the question :

1) I bought a (relatively) expensive laptop (17" 1000$) and upgraded the RAM from 8 to 16 GB so I can work with a lot of remote sessions and console programs, two or three virtual machines, a lot of tabs in the browser, etc. I also never miss an occasion to plug in an additional screen for more comfort. I think it is worth the money if, like me, you use your laptop for everything.

2) Get to know your system (and browser), and customize it. Use session managing tools. I'm using Opera as a navigator (it is very good but almost obsolete concerning html5 or plug-ins), and I make a heavy use of "browser sessions" (basically windows you can close and re-open later with all their tabs), built-in notes module, Keyboard shortcuts, and side panels. That way I can save some precious RAM while working on something else.

I also keep tabs in groups (Firefox should also be able to do that with the right extensions) it looks like this on Opera Web Browser.

Same goes for example for notes, console, file managers, etc. I use session tools (built-in, desktop widgets, etc) whenever possible. For example I can start Konsole with three different windows and multiple tabs, each tab/session with a different background color to better distinguish them, and with specific names to be able to distinguish them better. Sadly I don't know how to do similar things with Okular, even if I use it extensively too (although using tabs does help me organize things).

Using customizable mouse gestures while browsing can also help improve the efficiency.

As already mentioned the KDE activity feature can be very useful.

3) Using an efficient and customizable search tool and/or engine can also help. On KDE I often find it easier to use the desktop search tool (Alt+F2) to search for something in an opened window / application than to desperately search my task bar for a pdf file to find out I closed its Okular window 15 minutes ago.

On the Internet I've become used to DuckDuckGo to search on websites because of its useful "bangs" (for example typing "Napoleon !wfr" sends you directly to the article on the French Wikipedia). Now I even use it to search Google (!g !gfr !gde etc).

4) Keeping hands on the Keyboard and away from the mouse helps me. It's a matter of saving time rather than improving organisation, but it helps improving efficiency (I have 8 buttons on the mouse, more than 100 on my Keyboard).

5) Using a good File manager improved my efficiency. I'm no efficient user of Dolphin or Nautilus, but I found myself at ease with the orthodox file manager Krusader. I liked its tabs, protocol support, built-in terminal emulator for small tasks, and customization options. I use it a lot when it comes to inspecting server files etc. But there certainly is better software available.

6) General Task Management helps. I'm not very familiar with time/task management tools or techniques, but even keeping a simple text (sometimes shared with team members) or desktop post-it gadget where I write what I did, what I want to do, what I have to research, what I could not do, etc. helps closing the windows you know you won't use in the next hours.

Also, I often take notes with File links (one answer mentioned Evernote which is great) which removes the need to keep the file explorer window in parallel or the need to have extremely organized files and folders for temporary stuff.

As I said it's nothing advanced but it works at my level. Hope it helps.

It is difficult not to multitask in the modern environment. I think simplifying can be an answer to your question. Try to create good organized bookmark system. Using bookmarks can be a good way to reduce the amount of tabs on your browser.

Also general simplifying as one task per time is a good exercise to improve your productivity. I tend to use chrome for my work. It has all work bookmarked and organized. When I'm done with work, I open safari and use it for work non related stuff.

Genially speaking when you have less applications/programs running simultaneously you are unlikely to switch from unfinished task to another.

I usually creates list of things that I need to do and do it in the prioritized order. I use reminder app(iOS/mac. You can find tons of alternatives for Ubuntu) to note all tasks that I have to be doing. It helps you to track your progress and stay more organized. If a task is not simple, has subtasks. I tend to create a separate list for it and divide it into several smaller tasks.

After I started simplifying my work flow and reduced on multitasking I noticed how my productivity has raised. It is definitely worth giving this a try.

Bookmarking alternative

Emacs org-mode. Using org-protocol, you can add links to your notes. My browser bookmark bar is empty; I had hundreds of old archived bookmark files that I had little hope of getting through. I converted them to org-mode files (probably using pandoc), and quickly sorted, cleaned out and extracted what I might actually need.

So now, instead of adding bookmarks to my browser menus, I use org-store-link to embed in my org-mode notes. If I have too many browsers open, and need to put them away, I add them to my notes with, and add a remark that might help me remember what I might return to that site for.

(If you don't wnat to spend time learning Emacs and org-mode right now, you could simply paste your websites into a text file. For quickness, try Ctrl-l Ctrl-c in your browser. I also sometimes use Ctrl-s Ctrl-c Esc, but that is slooowww. For instance, notes could be

software - Ways to work well with my stack-like working habit on computer? - Personal Productivity Stack Exchange
http://productivity.stackexchange.com/questions/12033/ways-to-work-well-with-my-stack-like-working-habit-on-computer
(rad link on stack workflow) 

Of course, you may miss out on your notes being clickable from your editor, so maybe look for such feature.)

Edit: I just recently felt the need to solve the problem of having too many tabs open for org-protocol use to be convenient. In the case that I have more than a few tabs I want to make note of for later, I can use my browser to bookmark them as a set and export them to an html file. I then use pandoc to convert that file to org syntax and pipe it to the system clipboard, with

echo bookmarks.html | xargs pandoc --to=org --no-wrap | xsel -b

Finally, I simply paste the contents into the .org file where these bookmarks are relevant.

KDE

Also, I use kubuntu, which is Ubuntu with the KDE "desktop environment" (it's said to have grown beyond being simply a desktop environment). I use and love it's Activities feature, and cringe at the other OS' that don't have this. (Many have multiple desktops, but it's just not the same.

To facilitate using Activities, on my taskbar, besides the "Activities" widget, I've also added the "Activity bar".

So, some of my activities include, Todos, Tech, FB, Math, Main, Ent'mt and more (before a recent reinstall). It's rarely needed, but if an activity gets crowded, you can have multiple desktops within each.

Here is an image of my panel:

You can see my activities are quickly accessible to me (Super+Tab and Super+q are quick-keys). Also, zoomed in so you can see them better:

My use of Activities is very simple, I have not customized them besides those icons you see. I only take them as far as having designated "desktops" (really each "Activity" can have multiple desktops) for different activities. That is useful enough.

Virtual file tags

Recently I thought about having a way to tag files, that wouldn't rely on learning something new and/or installing special functionality. I thought about adding tags to files manually, and perhaps grepping for those tags, but what if I wanted to tag a file that was a PDF or image or otherwise not really greppable?

So, I used org-mode to create an outline that mirrored the directories and files that I felt were sugnificant, than used org-mode's awesome tagging feature to "group" locations and documents by topic.

Emacs dired as file explorer

I decided, while dolphin is nice, I didn't want to have to open it if I already had Emacs open and felt like using dired. I can't remember where I stole this, but currently I like it, I use C-u RET to open a link, and the system will use the default application to open, for instance, a PDF or Spreadsheet:

(defun my-dired-find-file (&optional prefix)
  (interactive "P")
  (if prefix
      (org-open-file (dired-get-file-for-visit) 'system)
    (dired-find-file)))
(define-key dired-mode-map "\r" 'my-dired-find-file)

tangent?

It's late, I veered away from your question. But the file exploring relates to SeanC's advice to open a file as you need it. (You can create links to files in org-mode, like file://~/.emacs, or [[~/.emacs][config]].)

I agree with the todotxt advice, I use it sparingly. It can cluttered, so I try to keep it empty often. There's an Emacs mode for it, and phone apps of course.

I'm also looking for ways to try out the Pomodoro technique in a sustainable way. There seems to be a shortage of quality affordable vibrating watch timers, or apps that are cross platform from PC to phone.