I reorganize (or tidy-up) my Windows config every week or so. About 30-45 minutes total work (including defragging the new config of mass directories and such).
Here is how I do it:
Desktop contains ONLY the Recycle Bin. Everything else is
A) Put on my RocketDock (for games/extremely commonly used items), and I find it in the Start Menu and put it in the root of the start menu's All Programs folder (On XP, I also organized my Start Menu by Name, but if you check all the options (I am too lazy to find out exactly what one, and all = less crap) in CCleaner it does it for you

)
B) Deleted, and I find it in the Start Menu and put it in the root of the start menu's All Programs folder (On XP, I also organized my Start Menu by Name, but if you check all the options (I am too lazy to find out exactly what one, and all = less crap) in CCleaner it does it for you

)
My Documents contains...
mostly crap programs put in there (*ehem* Screenshot Captor *ehem*...

)
contains some random temporary text files for temporary (duh) usage later.
My Music...
duh
My Videos...
(see above)
C:\Program Files - ONLY programs (and Windows crap). I use default directories on MOST things (that I can recognize) although having company names filling my Program Files folder is a big no-no for me.

C:\Games - ONLY Games (and Xfire/Fraps)
I also clean the drive root itself a lot, deleting the temporary windows crap that gets dropped in there in folder "35834953784bg98hr9gh39g8h84hy_update_kb1903478h" or something, and never removed by Microsoft's wonderful Windows Installer...
I check my startup proggies with StartupRun as well, crap gets in there randomly and its a pain. I have about 8 programs average booting with windows (Windows Sidebar, TrayIt, Taskbar Shuffle, L33tSig, Xfire, Xfire Music Plugin, and a couple others). Any more and I get picky.
As far as backups go, I dual partitioned my HDD, 20/120GB for backups, rest for my normal drive. Nightly auto backups of my C:\User\Brandon (I am on Vista, it is C:\Documents and Settings\Brandon on XP) and manual backups of new program versions reside on partition B. The good thing about this is I can wipe Vista at any time. The bad news is, if the whole drive goes belly up, I'm screwed

.
So yea, a bare-minimum Start menu, game-coated RocketDock and empty desktop/taskbar fill my screen. Uhh....maybe a little bit too tidy? Oh well, works for me!
