I've reorganized my music a few times, and it took me a while to get organized enough to want a single directory tree that held everything I owned. Every once and a while I go through the junk drawer and move a few more songs into the "official" tree, checking their metadata and whatnot. I was getting annoyed at finding duplicate songs in several junk drawers, so I wrote up a little script, find duplicates.py which can compare SHA1s for files in two trees and remove any duplicates from the lesser tree. Now there is a lot less junk to merge into my official tree.