There are really too many for me to give a definitive list, but here are a few that I'm confident with:
Top Three:
1. Earthbound (SNES)
2. Final Fantasy VII
3. Metal Gear Solid (the original PSX version. The Twin Snakes was good, but I didn't care for a few of the changes, namely that Baker no longer says "BLEEDING-HEART LIBERALS" with such disgust. That part always made me laugh.)

Others:
The Legend of Zelda: A Link to the Past (and the rest really)
Super Mario Brothers (and those that followed, especially SMB 2)
Super Metriod
Xenogears
Final Fantasy Tactics
Chrono Trigger
Starcraft and Broodwars
Serious Sam
EA Sports Rugby 2006
Tiger Woods PGA Tour 2005

I'm sure there are more.