G-man,
I do use some sub-folders under those I listed, but those are very very specific within the parent folder. For instance If you went into my University parent you would find the previously given list... then if you went into the PhD sub folder you would find the following:
-fall 2005 traffic pictures
-spring 2006 traffic pictures
-summer 2006 traffic pictures
-fall 2005 traffic results
-spring 2006 traffic results
-summer 2006 traffic results
-summer 2006 game field pictures
-summer 2006 game field results
-summer 2006 verdure results
-Manuscripts
-Abstracts
-Proposals
-China/Bien
-Protocols
-Plot plans
-Paper research

There are also some misc flotsom floating around within the PhD folder, but not much...if there's too much noise I can't find things easily (though I do have spotlight, it really is just easier for me to go look myself than looking through spotlight results). So I may be over-organized in that way, but I'd rather have 7 folders with 1 or two files in them than 20+files floating in one folder.
Does that help?
good luck!!
Theresa