I have them organised in FontExplorer in categories by kind: Serif, Non-serif, Fantasy (for symbols etc.), scripts and bitmap fonts.
This is initially all done by hand, and yes it can be a lot of work but it pays off. You really get to know what you have, and now helps me find fonts with a specific character very quickly.
FontExplorer is like iTunes for fonts. Main folders are used for categories above. Other than that I also keep collections (like playlists in iTunes) based on the fonts used per client.
It's what you personally like best of course.