Man, too many come to mind. I think I'll list the ones that I haven't used and haven't gotten much real inspiration out of (even if I liked the book).
Arcana Unearthed - Like the feats, absolutely adore the magic system, and the classes are alright, but besides giant I don't really like the races and the armor system is meh. Plus I don't know enough people who are interested in playing it anyway.
Ghostwalk - Interesting concept, nice world, and I really don't mind resurrections, but the main concept just seems a little... odd to me -- I can't quite put my finger on it. Also, can't say I like the fact that you can't have more eidolon/lancer levels than regular levels (though that is easily remedied with house ruling).
Fiend Folio - Just never found anything in there I really needed.
Savage Species - Same, but I must say the Emancipated Spawn is really hot.
Stronghold Builder's Guide - Really neat book, but nothing in it I couldn't live without. I would like playing a char sometime with the Landlord feat, though.