Here's the list of WotC Advanced and Prestige Classes. I don't have Weapons Locker or Menace Manual, but as far as I know, neither book had any classes in it. It also doesn't include anything from the Polyhedron Minigames.
Core Book:
Soldier, Martial Artist, Gunslinger, Infiltrator, Daredevil, Bodyguard, Field Scientist, Techie, Field Medic, Investigator, Personality, and Negotiator (Chapter 6: Advanced Classes)
Shadow Slayer, Occultist, Telepath, Battlemind, Mage, and Accolyte (Chapter 9: Campaign Models)
Urban Arcana:
Arcane Arranger, Archaic Weaponsmaster, Glamourist, Mystic, Shadow Hunter, Shadowjack, Speed Demon, Steet Warrior, Swashbuckler, Techno Mage, Thrasher, Wildlord, Archmage (PrC), Artificer (PrC), Ecclesiarch (PrC), and Holy/Unholy Knight (PrC)(Chapter 1: Characters)
Psionic Agent (Chapter 9: D&D and Urban Arcana)
Mastermind (PrC), Shapeshifter (PrC), Sniper (PrC), SpecOps (PrC), and Spellslinger (PrC)(Web Enchancement: More Prestigious)
d20 Future:
Ambassador, Dogfighter, Dreadnought, Engineer, Explorer, Field Officer, Helix Warrior, Space Monkey, Swindler, Technosavant, Tracer, and Xenophile (Chapter 1: Characters)
Bughunter, Dimension Ranger, Purifier, Concord Administrator, Star Law Officer, and Nuclear Nomad (Chapter 2: Campaigns)
Mecha Jockey (Chapter 9: Mecha)
d20 Past:
Explorer (Chapter 2: Rules Components)
Musketeer (PrC), Shaman, and Sorcerer (Chapter 3: Age of Adventure)
Fronteer Marshal (PrC), Mesmerist, and Spiritualist (Chapter 4: Shadow Stalkers)
Flying Ace (PrC), Gangster, and Scientist (Chapter 5: Pulp Heroes)