I attempt to keep my personal files, standalone/portable applications, and various other goodies in a single folder off the root. It makes it easier to move files between drives for backup purposes. Miscellaneous files are kept in the main folder. Stuff like TV shows I tend to keep on the desktop, since they're mostly the watch-then-delete type. Anything worth saving goes straight into the appropriate folder.
I realize this isn't the most effective organization structure, so any comments or suggestions would be appreciated.
+---3dsmax (Saved projects, textures, tutorials)
+---Comedy (Comedian albums, AVIs)
+---Fonts
+---Games (Game fixes, patches, DLC)
+---Music (Organized by artist, organized in foobar2000 by genre most of the time)
+---Pictures
| +---Comics
| +---Icons
| +---Photoshop
| \---Wallpaper
+---Porn Movies (Naughty videos)
+---Pornography (Naughty pictures)
+---Programs (Standalones, portable, and forced-portable applications)
+---Recipes (Pretty much saved webpages from goons with spoons)
+---Setup Files
| +---Codecs (Video, audio codecs filters and so on)
| +---Drivers
| +---Miscellaneous (Old programs that I hardly use, but may come in handy)
| +---Visual Styles (UX theme patcher, stylebuilder, and my only favourite visual style 'areao4' with some modifications)
| \---Windows Updates (I would integrate these onto the setup disc, but that's why theres service packs)
+---Video (Full videos, movies, tv shows)
| +---Brasseye
| +---Don Hertzfeldt
| +---Mystery Science Theater 3000
| \---Tim and Eric Awesome Show, Great Job!
\---Video Clips (FLVs and SWFs)
+---Enraging (clips that make me angry, but laugh at the same time)
+---Fat Pie
+---Opie & Anthony
\---Tim and Eric
Total size: 68GB