I organize manually as I rip them... genre, band, cd type, cd, etc.
iTunes has some option to sort things to folders based on the ID3 tags. Of course, if you don't have those or they're all fucked up (like Marlin, Marillion, Marillin... All the same band, spelled wrong, get different folders anyway) it can be a pain.
i made a little program for myself.. it was quite handy.. unfortunately i lost it when my harddrive crashed a couple of years ago.. since then, ive just been more organized in general.