I've been organizing my music files for years in an easy to follow directory structure, I'm so used to it that I actually find ipod searching annoying.
I use a structure of genre/artist/album and have all of my music named in the same convention of track# - title.
I know what music I have, and it's easy to find this article way, you just have to take the time, and potentially a lot of it, to get all of your files organized.
Cheers