Xenogears. The story is brilliant (and the gameplay seemed somewhat different from a traditional turn-based RPG, which is a plus in my book)!
Or Red Alert 2... Or The Legend of Zelda: Ocarina of Time/Majora's Mask... Or Gradius Gaiden... Or Metal Gear Solid... Can't decide! @_@
Random game thought :
Why is Bionic Commando Rearmed 2 getting so much hate? We finally get a real game and they're not even satisfied... I'm starting to hate the gaming community so f****** much...