I don't really. Well, not totally. What I do is:
1) Have 1 partition where windows goes. Certain things like Winrar will also get installed there, but only things that I usually don't access directly and are fairly small
2) All my Games/Apps get installed on other partitions
3) I have 1 Directory where all my downloads goes(also not on Windows partition). There are sub-directories in there for certain commonly related files for certain Apps(UT2k4 for eg)
4) I have 1 Directory where all my music goes
5) All my Apps/Games get installed by the App/Game name and not by Company/Publisher and FFS not under Program Files(a friend tried that and I just about lost my mind

)
6) Only rarely do I access EXE's directly from the Installed Directory or even the Program folder on Start menu. Commonly used Apps/Games are accessed through Quicklaunch.
7) I never use My Documents, or My Music, or any other Crappy directory in the Documents/Settings directories, unless an App/Game has put something in there. That setup is a complete mess and PITA.
8) Commonly used Documents also get a spot in the Quicklaunch menu
I suppose I organize more than I thought, but unlike Win 3.1 I really don't worry about tidying up my Directories list(s). Just a waste of time IMO.