| 1. | Naruto Shippuden: Ultimate Ninja Storm 2 | 3,296,077 | 12.16% | 21 | 5:44:18 |
| 2. | Kirby's Return to Dream Land | 1,763,100 | 6.51% | 5 | 1:17:34 |
| 3. | Pokémon Black and White | 1,150,570 | 4.25% | 2 | 31:02 |
| 4. | The Legend of Zelda: The Wind Waker | 1,105,817 | 4.08% | 10 | 2:49:28 |
| 5. | Kingdom Hearts 3D: Dream Drop Distance | 1,019,044 | 3.76% | 5 | 2:30:07 |
| 6. | Kingdom Hearts Birth by Sleep | 610,118 | 2.25% | 6 | 1:33:06 |
| 7. | Kingdom Hearts II | 552,545 | 2.04% | 8 | 2:03:39 |
| 8. | Persona 4 | 517,873 | 1.91% | 1 | 15:31 |
| 9. | Mega Man X: Command Mission | 517,334 | 1.91% | 2 | 1:00:02 |
| 10. | Naruto: Ultimate Ninja Storm | 428,243 | 1.58% | 4 | 1:13:39 |
| 11. | Mega Man Battle Network 5 | 409,072 | 1.51% | 1 | 15:11 |
| 12. | Naruto Shippuden: Ultimate Ninja Storm 3 | 405,762 | 1.50% | 1 | 30:32 |
| 13. | Mega Man Zero 2 | 404,281 | 1.49% | 2 | 28:59 |
| 14. | No More Heroes 2: Desperate Struggle | 403,972 | 1.49% | 3 | 46:32 |
| 15. | Kingdom Hearts Re:Chain of Memories | 358,651 | 1.32% | 4 | 1:02:04 |
| 16. | Naruto Shippuden: Ultimate Ninja Storm Generations | 347,394 | 1.28% | 3 | 1:30:03 |
| 17. | Mega Man Star Force 3 | 341,003 | 1.26% | 1 | 15:20 |
| 18. | Resident Evil Code: Veronica | 320,374 | 1.18% | 3 | 1:00:12 |
| 19. | Kingdom Hearts Final Mix | 313,086 | 1.16% | 1 | 15:02 |
| 20. | Mega Man Battle Network 3 | 312,881 | 1.15% | 1 | 15:13 |
| 21. | Mega Man Battle Network 2 | 281,183 | 1.04% | 1 | 15:11 |
| 22. | Mario & Luigi: Dream Team | 234,937 | 0.87% | 2 | 1:02:30 |
| 23. | The Legend of Zelda: Phantom Hourglass | 220,057 | 0.81% | 6 | 1:33:06 |
| 24. | Blue Dragon | 217,112 | 0.80% | 1 | 15:31 |
| 25. | Mega Man Star Force 2 | 184,226 | 0.68% | 3 | 45:41 |
| 26. | Klonoa 2: Lunatea's Veil | 181,593 | 0.67% | 8 | 2:03:48 |
| 27. | Metroid Prime 3: Corruption | 170,337 | 0.63% | 4 | 1:01:35 |
| 28. | The Legend of Zelda: The Minish Cap | 160,210 | 0.59% | 4 | 1:02:04 |
| 29. | Final Fantasy IX | 155,215 | 0.57% | 1 | 15:31 |
| 30. | Kirby: Canvas Curse | 139,431 | 0.51% | 1 | 15:30 |
| 31. | Mega Man Star Force | 118,465 | 0.44% | 1 | 15:11 |
| 32. | Final Fantasy IV | 114,005 | 0.42% | 1 | 15:31 |
| 33. | No More Heroes | 107,483 | 0.40% | 1 | 15:30 |
| 34. | Paper Mario | 105,453 | 0.39% | 5 | 1:15:00 |
| 35. | Mega Man Zero Collection | 104,673 | 0.39% | 7 | 1:47:28 |
| 36. | Kingdom Hearts | 99,158 | 0.37% | 1 | 15:31 |
| 37. | Paper Mario: The Thousand-Year Door | 94,611 | 0.35% | 8 | 2:03:45 |
| 38. | Super Mario RPG | 77,775 | 0.29% | 4 | 1:02:03 |
| 39. | Naruto: Clash of Ninja Revolution 2 | 62,935 | 0.23% | 1 | 15:31 |
| 40. | Persona 3 | 57,911 | 0.21% | 2 | 31:02 |
| 41. | The Legend of Zelda: Ocarina of Time | 56,320 | 0.21% | 1 | 15:30 |
| 42. | Final Fantasy Crystal Chronicles | 53,958 | 0.20% | 1 | 15:31 |
| 43. | The Legend of Zelda: Majora's Mask | 52,060 | 0.19% | 6 | 1:47:14 |
| 44. | Sonic Adventure 2 | 51,312 | 0.19% | 3 | 1:01:03 |
| 45. | Golden Sun: The Lost Age | 49,081 | 0.18% | 4 | 1:02:04 |
| 46. | Metroid Prime 2: Echoes | 46,327 | 0.17% | 2 | 30:46 |
| 47. | Mega Man X5 | 46,092 | 0.17% | 3 | 43:04 |
| 48. | Castle Crashers | 45,637 | 0.17% | 1 | 30:02 |
| 49. | The Legend of Zelda: Skyward Sword | 41,112 | 0.15% | 4 | 1:44:39 |
| 50. | Castlevania: Order of Ecclesia | 40,713 | 0.15% | 1 | 15:31 |
| 51. | The Legend of Zelda: Twilight Princess | 39,817 | 0.15% | 5 | 1:17:35 |
| 52. | Super Paper Mario | 39,668 | 0.15% | 3 | 46:32 |
| 53. | The Legend of Zelda: Spirit Tracks | 37,780 | 0.14% | 3 | 46:32 |
| 54. | Golden Sun: Dark Dawn | 37,416 | 0.14% | 11 | 2:50:10 |
| 55. | Mega Man Legends 2 | 36,353 | 0.13% | 3 | 45:34 |
| 56. | Final Fantasy III | 36,077 | 0.13% | 1 | 15:31 |
| 57. | Kingdom Hearts 358/2 Days | 32,036 | 0.12% | 4 | 1:01:39 |
| 58. | Breath of Fire III | 27,838 | 0.10% | 3 | 46:03 |
| 59. | Sonic Unleashed | 27,600 | 0.10% | 2 | 31:02 |
| 60. | Metal Slug 5 | 27,390 | 0.10% | 1 | 15:31 |
| 61. | Kingdom Hearts Re:coded | 25,818 | 0.10% | 1 | 15:31 |
| 62. | Mega Man Zero 4 | 25,119 | 0.09% | 2 | 31:02 |
| 63. | Sonic Generations | 24,310 | 0.09% | 5 | 1:32:04 |
| 64. | Kirby: Nightmare in Dream Land | 22,680 | 0.08% | 1 | 15:31 |
| 65. | Nier | 22,338 | 0.08% | 2 | 31:02 |
| 66. | Pokémon Colosseum | 21,104 | 0.08% | 2 | 31:02 |
| 67. | Mega Man X8 | 20,301 | 0.07% | 2 | 30:32 |
| 68. | Onimusha: Dawn of Dreams | 17,432 | 0.06% | 1 | 15:31 |
| 69. | The Legend of Zelda: Oracle of Ages | 17,086 | 0.06% | 2 | 31:02 |
| 70. | Naruto Shippuden: Clash of Ninja Revolution 3 | 16,040 | 0.06% | 1 | 15:05 |
| 71. | Kirby Super Star Ultra | 15,334 | 0.06% | 2 | 31:02 |
| 72. | Attack on Titan 2 - A.O.T.2 | 14,955 | 0.06% | 1 | 15:30 |
| 73. | Brave Fencer Musashi | 14,205 | 0.05% | 5 | 1:17:34 |
| 74. | Boktai 3: Sabata's Counterattack | 13,634 | 0.05% | 3 | 46:31 |
| 75. | Sonic Advance | 12,769 | 0.05% | 5 | 1:17:33 |
| 76. | Mega Man Legends | 12,261 | 0.05% | 1 | 15:03 |
| 77. | Kirby's Epic Yarn | 11,563 | 0.04% | 2 | 31:02 |
| 78. | Pokémon HeartGold and SoulSilver | 11,442 | 0.04% | 3 | 46:33 |
| 79. | Final Fantasy VI | 10,086 | 0.04% | 1 | 15:30 |
| 80. | Onimusha 2: Samurai's Destiny | 9,977 | 0.04% | 1 | 15:31 |
| 81. | Final Fantasy XI | 9,106 | 0.03% | 1 | 15:31 |
| 82. | Naruto: Ultimate Ninja 3 | 7,003 | 0.03% | 1 | 15:31 |
| 83. | Super Mario Galaxy 2 | 6,858 | 0.03% | 1 | 15:31 |
| 84. | Kirby & the Amazing Mirror | 6,606 | 0.02% | 1 | 15:31 |
| 85. | Sonic the Hedgehog | 6,159 | 0.02% | 1 | 15:31 |
| 86. | Shadow the Hedgehog | 6,058 | 0.02% | 3 | 1:00:52 |
| 87. | Castlevania: Curse of Darkness | 5,235 | 0.02% | 1 | 30:01 |
| 88. | Kirby 64: The Crystal Shards | 5,019 | 0.02% | 2 | 31:02 |
| 89. | Mario & Luigi: Bowser's Inside Story | 4,800 | 0.02% | 1 | 15:31 |
| 90. | Final Fantasy VIII | 4,654 | 0.02% | 1 | 15:30 |
| 91. | Gunstar Heroes | 4,580 | 0.02% | 4 | 1:02:04 |
| 92. | Atelier Iris 3: Grand Phantasm | 4,310 | 0.02% | 3 | 46:18 |
| 93. | Kirby's Dream Land 3 | 4,288 | 0.02% | 1 | 15:31 |
| 94. | Phantasy Star IV | 4,265 | 0.02% | 1 | 15:31 |
| 95. | Super Smash Bros. Brawl | 4,251 | 0.02% | 1 | 15:30 |
| 96. | Sonic and the Secret Rings | 4,171 | 0.02% | 1 | 20:00 |
| 97. | Boktai 2: Solar Boy Django | 4,056 | 0.01% | 1 | 15:31 |
| 98. | Dragon Ball Z: The Legacy of Goku II | 4,000 | 0.01% | 2 | 30:39 |
| 99. | Final Fantasy IV: The After Years | 3,983 | 0.01% | 2 | 30:34 |
| 100. | Mega Man X4 | 3,255 | 0.01% | 1 | 15:31 |
