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Funnily enough I just organised them yesterday. 1200. I keep them in a rough classifications with some for current jobs.
 

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I don't organise my fonts. Linotype does. It's great. You don't still organise your music by hand, do you?

Seriously though, an online database reference would be great. Why fonts were never created with a meta file containing all the relevant info (serif/san-serif, grotesque, etc.) is beyond me.
 
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.
 
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