Ill go by year. Backwards. Because memory. Also as I go down its gonna be harder and harder to only pick one.
2003 - Knights of The Old Republic
2002 - Kingdom Hearts
2001 - Halo Combat Evolved
2000 - Tie between Banjo Tooie and Spyro Year of The Dragon
1999 - HUGE tie between Super Smash Bros, Silent Hill, Ape Escape, Resident Evil 3: Nemesis, Pokemon Yellow, and Spyro 2 Ripto's Rage (1999 was a fucking great year for playstation and nintendo!!!)
1998 - Another big one - Resident Evil 2, Parasite Eve, Jersey Devil, Banjo Kazooie, Heart of Darkness, Spyro the Dragon, Medievil, Metal Gear Solid, Crash Bandicoot 3, Turok 2, Grim Fandango, and Tomb Raider III
1997 - Mario Kart 64, Oddworld Abe's Oddysee, Croc, Crash Bandicoot 2, Tomb Raider II
1996 - Resident Evil, Pokemon Red, Kirby Super Star, Super Mario 64, Crash Bandicoot, Twisted Metal II, Tomb Raider
1995 - Earthbound, Yoshi's Island, Twisted Metal, Worms