Fantasy Flight and Atlas
Fantasy Flight Games Materials also gets a lot of use. In particular, Seafarer's Handbook, Spells and Spellcraft, Path of Magic, Path of the Sword and Monster's Handbook see a lot of use. Occult Lore by Atlas Games has also been an indispensible resource.
Here is a list of the non-WotC books I use, in the order of usefulness.
1. Path of Magic (fantasy flight games)
2. Monster's Handbook (fantasy flight games)
3. Spells and Spellcraft (fantasy flight games)
4. Occult Lore (Atlas Games)
5. Unveiled Masters: The Essential Guide to Mind Flayers (Paradigm concepts)
6. Relics and Rituals (Sword and Sorcery Studies)
7. Encyclopedia Arcane: Chronomancy (Mongoose)
8. Encyclopedia Arcane: Chaos Magic (Mongoose)
9. The Book of the Righteous (Green Ronin)
10. Book of Erotic Fantasy (Valar)
11. Nyambe: African Adventures (Atlas)
12. Rokugan (AEG)
13. Relics and Rituals II (Sword and Sorcery Studios)
14. Encyclopedia Divine: Fey Magic (Mongoose)
15. Path of the Sword (Fantasy Flight Games)
16. Traps and Treachery (Fantasy Flight Games)
17. Creature Collection (Sword and Sorcery Studios)
18. Creature Collection II (Sword and Sorcery Studios)
19. Monsters of the Mind (Green Ronin)
20. Quintessential Drow (Mongoose)
21. Seafarer's Handbook (Fantasy Flight Games)
22. Requiem for a God (Monte Cook)
23. Nyambe: Ancestral Vault (Atlas)
24. Book of Eldritch Might 1, 2 and 3 (Monte Cook)
25. Book of Hallowed Might (Monte Cook) - considering removing as too powerful.
I also make heavy use of Call of Cthulhu, although that is technically a WotC book.
These following two haven't been around long enough to have made a major impact, but they probably will:
1. Conan the Roleplaying Game (Mongoose)
2. The Scrolls of Skelos (Mongoose)
3. Mindshadows
4. Torn Asunder: Critical Hits
The most useless book I ever bought was the Slayer's Guide to Yuan Ti by Mongoose. (The presentation of the Yuan Ti in Dragon 305 is FAR superior and more in keeping with my own Cthulhu-ish vision for Yuan Ti).
Of course, I still make far more use of other source materials than d20 books. My players are an incredible source of inspiration. Also, the films I watch and the books I read are much more influential in my games than any of the books above. Most notably the writings of Robert E. Howard, Clark Ashton Smith, HP Lovecraft, Mary Shelley, Alexander Dumas, Edgar Rice Burroughs, William Peter Blaty, Brian Lumley, Edith Wharton, Lloyd Alexander, Shirley Jackson, Sir Arthur Conan Doyle, Edgar Allan Poe, Shakespeare, and Bram Stoker are the most evident in my games, I think. Old Hammer and Universal monster movies, Spaghetti Westerns, Roger Corman movies, Indiana Jones, Star Wars and Errol Flynn movies are constant sources of inspiration. Television shows such a Dark Shadows, the A Team, and others have also found their spots in my games. Comic books are yet another source. And, of course, music lyrics have inspired entire cycles of games (a good mixture of Lovecraft and KISS makes for an interesting pantheon of gods).
Magazines are also a good source of inspiration for me. Of course, speaking on non-WotC sources, that now includes Dungeon and Dragon, but I also have found inspiration within Cosmopolitan, Weird Tales, Teen, 17, Maxim, Stuff, Playboy, Penthouse, Signs and Portents, People, Harper's Bazaar, and Elle.
What non-WotC books are you using?