Wikipedia
List of Prestige Classes lists PRCs by source.
Picking out modules:
Return to the Temple of Elemental Evil - Doomdreamer (3.0)
Expedition to Castle Ravenloft - Knight of the Raven
Expedition to the Demonweb Pits - Demonwrecker / Jaunter
Shattered Gates of Slaughtergarde - Dark Scholar / Serene Guard / Solar Channeler / Twisted Lord
Dragon magazine has published over 200 prestige classes. Many of these prestige classes were reprinted in sourcebooks later.
274 The Mystic
275 The Duelist
280 Divine Champion / Eldritch Master
281 Zerth Cenobite / Arcanopath Monk / Truth Seeker / Psi-hunter
282 Blessed of Gruumsh
283 Shining Blade of Heironeous / Radiant Servant of Pelor / Fleet Runner of Ehlonna / Mighty Contender of Kord / Flame Steward
284 Dragonkith
285 Lightbearer / Silverstar
286 Elder Druid / Nightcloak
287 The Athar / The Cipher / The Sensate / The Sinker / The Taker / The Xaositect / Fiend Slayer / Dreadmaster
288 Lifedrinker
289 Poison Fist / Ghost-faced Killer / Weightless Foot
290 Justicar / Dancer of Sharess
291 Gnome Giant Killer
292 Cave Stalker / Fiend Binder / Prairie Runner / The Darkwood Stalker
293 Nightsong Enforcer / The Glaive of Azharadian
294 Windsinger / Nightsong Infiltrator / The Green Hunter
295 Primal Rager / Fierce Grappler / Brawler / Master Siege Engineer
296 Dragonscribe / Knight of the Scale / Heartseeker / Vengeance Sworn / Dragon Mystic / Sphere Minion / Illithidkin / Snake Servant / Waker of the Beast / Acolyte of the Fist
297 Shadar Sentinel / Soulreaver / Arcane Lord / Bow Master / Perfected One / Stalwart Warden / Unholy Ravager / World Guardian / Master of the Secret Sound / Knight of the Chase
298 Deep Avenger / Gloomblade / Gray Sage / Bloodsister / Nightshade / Kabuki Warrior / Dragon Warrior
299 Reaper's Child / Monk of the Enabled Hand / Dwarven Thane / Orc Blademaster
300 Faceless Ones / Deep Thrall / Shoal Servant / Tiger Mask / The Flesheater
302 The Tainted / Mask of Johydee
307 Battlepriest of Cormyr / Council Mage of Cormyr / Noble Adventurer / Moon Drover of Cormyr / Royal Scout of Cormyr / Whitehorn / Follower of the Skyserpent / Tree-Friend / Artist's Vengeance / Ranger of the Night’s Watch
308 Aeromancer / Ordinator / Empowered
310 Branch Dancer / Mole / Jobber / Magic Filcher / Stoneface
311 Battle Howler of Gruumsh / Green Whisperer / Memory Smith / Metal Master / The Mourner / Worldspeaker
312 Oppressor / Poisoner / Replacement Killer
313 Mind Mage
314 Heartfire Fanner / Master of the North Wind / Master of the South Wind / Master of the East Wind / Master of the West Wind / Darkwater Knight / Earthshaker / Firestorm Berserker / Icesinger / Purebreath Devotee
315 Silverhair Knight / Companion of the Dead / Shark Cultist / Harmonium Peacekeeper / Anarchromancer / Omatu Master / Eagle Knight / Jaguar Knight / Boge of Nomog-Geaya
316 Master Inquisitive
317 Osteomancer / Flux Adept / Cerebrex / Ranger Knight of Furyondy / Battleguard of Tempus
318 Scout Warlord / Battlemage Warlord / Driven Leader Warlord
319 Aerial Avenger / Shen
321 The Infused / Barber / Corsair / Holy Slayer / Mamluk / Arvoreen's Keeper / Arvoreen's Warder
322 Shadow Apostle / Deathstalker of Bhaal
323 Spirit Speaker
324 Sworn Slayer
325 Bowman Charger
326 Shaper of Form
328 Chimeric Champion of Garl Glittergold / Itinerant Warder of Yondalla / Justice Hammer of Moradin / Mystic Keeper of Corellon Larethian / Force Missile Mage
329 Thrall of Pazuzu
330 Jester
333 Thrall of Fraz-Urb'luu
335 Charlatan
337 Thrall of Zuggtomy
338 Wormhunter
339 Incantifier / Son of Mercy
340 Master Astrologer
341 Thrall of Baphomet
345 Thrall of Kostchtchie
349 Thrall of Dagon
353 Thrall of Malcanthet
354 Totemic Demonslayer
357 Spell Sovereign / Thrall of Demogorgon