Hive: HKEY_LOCAL_MACHINE
Key: Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell
Folders
Under this key, you will find a set of values of type REG_EXPAND_SZ. For example, for the value of Start Menu is %USERPROFILE%\Start Menu. On my workstation %USERPROFILE% is C:\WINNT\PROFILES\Wayne. You can change the location of the special folders by change the value of the environmental value or by hacking the appropriate registry value.