This list is getting really bloated really fast so feel free to point out any mistakes I may have made.
Final Fantasy VII 7
Final Fantasy X 6
Final Fantasy IX 5
Fire Emblem: Path of Radiance 5
Metal Gear Solid 3 5
Mother 3 5
Super Mario 64 5
Donkey Kong Country 2 4
Final Fantasy Tactics 4
Final Fantasy VI 4
Okami 4
Phoenix Wright: Ace Attorney: Trials & Tribulations 4
Skies of Arcadia 4
Tales of Vesperia 4
The Legend of Zelda: Majora's Mask 4
Uncharted 2: Among Thieves 4
Bioshock 3
Disgaea: Hour of Darkness 3
Earthbound 3
Half-Life 2 3
Killer7 3
Metal Gear Solid 2: Sons of Liberty 3
Metroid: Zero Mission 3
Nier 3
Pokemon Red/Blue/Yellow 3
Professor Layton and the Unwound Future 3
Shin Megami Tensei: Persona 4 3
Super Mario World 2: Yoshi's Island 3
Super Street Fighter IV 3
The Legend of Zelda: A Link to the Past 3
The Secret of Monkey Island 3
TimeSplitters: Future Perfect 3
Dark Cloud 2
Devil May Cry 3 2
Dragon Quest VIII: Journey of the Cursed King 2
Eternal Darkness: Sanity's Requiem 2
Ever17 -the out of infinity- 2
Final Fantasy VIII 2
Fire Emblem 2
Ghost Trick 2
Grand Theft Auto: San Andreas 2
Hotel Dusk: Room 215 2
Jet Force Gemini 2
Kingdom Hearts 2
Mass Effect 2 2
Phoenix Wright: Ace Attorney 2
Resident Evil 4 2
Shadow Hearts: Covenant 2
Shin Megami Tensei: Devil Survivor 2
Shin Megami Tensei: Persona 3 2
Silent Hill 2 2
Sly 2: Band of Thieves 2
Sonic 3 & Knuckles 2
Soul Calibur II 2
Spyro the Dragon 2
Star Ocean: The Second Story 2
Super Mario Bros. 3 2
Super Mario World 2
Super Smash Bros. Melee 2
Tales of the Abyss 2
The Legend of Zelda: Ocarina of Time 2
The Legend of Zelda: The Wind Waker 2
The Legend of Zelda: Twilight Princess 2
Umineko no Naku Koro ni 2
WarioWare: Twisted! 2
--
Black Turtle did a pretty good job.