This is gonna be tough, but I'll try.
1. Super Mario 64
2. Super Smash Bros. Brawl
3. The Legend of Zelda: A Link to the Past
4. Star Fox 64
5. The Legend of Zelda: Wind Waker
6. Super Metroid
7. Super Mario World
8. Metroid Prime
9. The Legend of Zelda: Twilight Princess
10. Phoenix Wright Ace Attorney: Trials & Tribulations
11. Metroid Prime 3: Corruption
12. Sonic 3 & Knuckles
13. Final Fantasy VIII
14. Resident Evil 4: Wii Edition
15. Mystical Ninja: Starring Goemon (N64)
16. Donkey Kong Country 2: Diddy's Kong Quest
17. Final Fantasy X
18. Metal Gear Solid 3
19. Castlevania: Portrait of Ruin
20. Mario Kart 64
... as I said, it's very hard. Can't really be sure, but all of those would be in my top 30 anyway.
Top 5 this gen...
1. Super Smash Bros. Brawl
2. The Legend of Zelda: Twilight Princess
3. Metroid Prime 3: Corruption
4. Resident Evil 4: Wii Edition (I had never played RE4 on GC/PS2, so it was epic to me)
5. Super Mario Galaxy
