My favorite publishers would be:
-Kenzer & Co. (I love the Kalamar setting and the books for it never lack for detail)
-AEG (Spycraft, Rokugan, and the single-word-title series are consistently impressive)
-Sword & Sorcery Studios (Scarred Lands is amazing; who'd have thought Greek mythology could inspire THAT sort of setting?)
Most of these are not 3.5 books, but the recent revision to the core rules are not really significant when it comes to supplimental sources. Only the books that are rules-intensive/story-light are really affected by the 3.0/3.5 distinction, and I have hardly ever bought anything like that, anyways.