I may have the messiest workstation, but my drives are as neat as a pin........
I don't have my OS and my Program Files on seperate partitions. I have an extra HDD dedicated to a clone copy of that partition so I guess there is no need.
My D:/ drive is My Documents. This is my original from way back, so it is not the "My Documents" that XP tries to put everything into. But I always just navigate to it myself. In here I have all the typical folders. The main one I use is Misc. Documents. This is my junk drawer. It is broken up into numerous sub folders. If I find myself gathering too many of a certain type of file (i.e. gifs, funny pics, etc.) I will make a folder and shove everything into it, but more important, I will put all new files in there as well.
My E:/ drive is downloads, my F:/ drive is music and my G:/ drive is Setups. Whenever I download, unzip or aquire any program, I create a Folder with the program name and all versions past and present go into that folder. I always can find my latest version easily this way.
I may not be able to find a CD, DVD or even a pencil at my desk, but ask me for any file or folder on my computer and I'll have it for ya in 30 seconds or less.