**In order (as of now...the top one is ALWAYS the top game, though))**
1. Final Fantasy IV
2. Chrono Trigger
3. Mega Man 2
4. Final Fantasy VII
5. Metal Gear Solid 3
6. Super Metroid
7. Super Mario Bros. 3
8. The Legend of Zelda: Ocrina of Time
9. Chrono Cross
10. Ace Combat 2

RUNNER UPS (no order at all/some of these used to be in the top 10): Knights of the Old Republic, Metroid:Zero Mission, Super Mario World, Metal Gear Solid, Xenogears, The Legend of Zelda:Link to the Past, Castlevania: Symphony of the Night, and others I can't think of right now.