Hmm... First time I coinsidered voting in this.
1. Pokemon RBY
2. Chrono Trigger
3. Super Metroid
4. Super Mario 64
5. Final Fantasy VI
6. Paper Mario
7. Super Mario Bros. 3
8. MGS3: Snake Eater
9. Super Mario World
10. Zelda: OoT
10. Yoshi's Island
11. Resident Evil 4
12. Super Mario RPG
13. Metroid Prime
14. Tales of Symphonia
15. SoulCalibur II
16. SSBB
17. Super Mario Galaxy
18. Wind Waker
19. DKC2
20. Majora's Mask
21. Fire Emblem 7
22. Star Fox 64
23. Pokemon BW
24. Metal Gear Solid
25. Mega Man 2