Why?
I put my important documents, like PDF files of my taxes, phone numbers, personal project and papers I write in Word in the My Documents folder. My C drive is for all the ultra important programs and documents that I need for keep my computer and life running. Those documents belong in the "My Documents" folder and belong on my C drive.
My D drive is for my entertainment based media files: MP3s, AVIs MPEGs, JPEGs, gaming PDFs, and whatnot.
My E drive is for my games. I have all my games installed on my E Drive. Fallouts, Baldur's Gates, NWNs, KotORs, Morrowind, Oblivion, and what not. My E drive is meant for my games.
My F drive is or unsorted miscellaneous Internet files and logs, temporary stuff.
This is how I organize my computer. I don't give a bloody hell about Unix, Microsoft, and any bullcrap like that. This is how I organize stuff and it has worked for me for years.