I liked all of the Tome of Horrors books (I, II, & III). ToH I had a 3.5e revision, though I think it was only PDF.
Green Ronin's Advanced Bestiary is a book of templates, but they let you make some really interesting critters; Paizo's used it a few times in their adventures, IIRC.
Most of the rest of the monsters I used were 3e conversions, or from WotC, or modifications thereof.
Edit: Almost forgot -- Monsternomicon got a 3.5e-ization, too. The Monsternomicon has some really interesting monsters, but they never seem to fit what I wanted, so I don't think I got the 3.5e version.
Edit 2: Necromancer also did the Mother of All Encounter Tables, which I used for inspiration a couple of times. If you want to use random rolls to populate areas, it could be a useful starting place.