Here's my top 50 thus far:
50. A Link Between Worlds
49. Sonic The Hedgehog 2
48. Pokemon Red/Blue
47. Persona 2 - Eternal Punishment
46. Mario Kart Double Dash
45. Kirby Air Ride
44. Batman: Arkham City
43. Fire Emblem: Awakening
42. Link's Awakening
41. Super Mario Galaxy
40. EarthBound
39. Fire Emblem 7
38. Zelda 2
37. Metroid Fusion
36. Uncharted 2
35. Fire Emblem: Path of Radiance
34. Trauma Center: Second Opinion
33. Trauma Center: Under the Knife 2
32. Skyward Sword
31. Phoenix Wright: Ace Attorney
30. Shin Megami Tensei: Nocturne
29. Metroid Prime 3
28. Pokemon Gold/Silver
27. The Last of Us
26. Twilight Princess
25. Super Mario Galaxy 2
24. Metroid Zero Mission
23. The Minish Cap
22. Super Smash Bros Melee
21. The Legend of Zelda
20. Fire Emblem: Radiant Dawn
19. Phoenix Wright: Ace Attorney - Trials and Tribulations
18. Super Mario Sunshine
17. Metroid Prime 2
16. Final Fantasy 6
15. Persona 4 Golden
14. Tales of Symphonia
13. Shadow of the Colossus
12. Mother 3
11. Wind Waker
10. Super Metroid
9. Super Mario World
8. Link to the Past
