This was my list. Now, I may just focus on True20 and third party d20M instead.
WOTC (The following are pretty much all of the books outside of Arms and Equipment Guide, Book of Vile Darkness, and Unearthed Arcana that I actually really like or like enough that I consider to be worth owning/buying)
3.0: MM2, Fiend Folio
3.5 Dragonomicon, Fiendish Codex I, Lords of Madness, Heroes of Horror, Stormwrack, Complete Warrior, PHB2, Spell Compendium ( for the domains and many of the spells)
Non WOTC
Adamant: Hot Pursuit
Chanimail Bikini/Goodman Games: Beyond Monks
Green Ronin: Advanced Bestiary, Cavalier's Handbook, Holy Warrior's Handbook
Lion's Den: Fey
Malhavoc: Book of Iron Might, Book of Roguish Luck
Mongoose: Quintessential Monk, Quintessential Rogue, Quintessential Sorcerer, Quintessential Wizard
Mystic Eye Games: Artificer's Handbook
Second World Simuations: Skill Focus Talking
Skirmisher: Experts