My server is setup like this.
Drive 1 is a 1TB split into 2 partitions. 1 80GB and the rest free.
80GB = Windows
920GB Music folder / TV Shows / Digital Books
Music:
Artist / Album (plus cover art) / song list
TV Shows:
Title / Season / Episodes
eBooks:
Title / File (plus cover art)
Drive 2 (2TB) = Movies (also contains my incoming folder, and converted movie folder)
Movies:
Name (quality and year) / File + Cover Art (if possible)
Drive 3 (2TB) = Games / Apps / Steam Folder
Games are ISO's inside a Game folder
Apps:
Name / App plus any other file associated with it
All of my drives are almost full so I plan on adding another 2TB to the mix sometime soon. I also have other stuff on there too, but can't talk about the other stuff on the forums.