| 1. | Advance Wars | 321,897 | 9.17% | 108 | 1:08:51:01 |
| 2. | Digimon World | 274,097 | 7.81% | 34 | 4:55:52 |
| 3. | Pokémon Red and Blue | 217,448 | 6.20% | 12 | 5:14:43 |
| 4. | Battalion Wars 2 | 179,850 | 5.12% | 39 | 10:46:37 |
| 5. | Fire Emblem: The Binding Blade | 166,782 | 4.75% | 45 | 1:09:53:59 |
| 6. | Phoenix Wright: Ace Attorney | 152,022 | 4.33% | 10 | 3:56:03 |
| 7. | F-Zero X | 138,731 | 3.95% | 8 | 3:07:30 |
| 8. | Advance Wars 2: Black Hole Rising | 119,294 | 3.40% | 76 | 1:06:58:28 |
| 9. | Super Mario Bros. | 101,056 | 2.88% | 6 | 1:02:35 |
| 10. | F-Zero: GP Legend | 94,358 | 2.69% | 13 | 4:15:29 |
| 11. | Mega Man Legends 2 | 88,145 | 2.51% | 44 | 11:04:50 |
| 12. | F-Zero | 83,486 | 2.38% | 11 | 3:28:44 |
| 13. | F-Zero GX | 78,542 | 2.24% | 11 | 2:45:31 |
| 14. | Mega Man Battle Network | 56,778 | 1.62% | 13 | 1:44:24 |
| 15. | Fire Emblem Gaiden | 49,818 | 1.42% | 4 | 58:53 |
| 16. | Super Famicom Wars | 47,647 | 1.36% | 4 | 32:52 |
| 17. | Yu-Gi-Oh! Dungeon Dice Monsters | 43,098 | 1.23% | 1 | 9:50 |
| 18. | Field Commander | 39,629 | 1.13% | 12 | 5:31:44 |
| 19. | Game Boy Wars 3 | 37,198 | 1.06% | 16 | 7:51:17 |
| 20. | Advance Wars: Dual Strike | 36,534 | 1.04% | 55 | 17:21:09 |
| 21. | Yu-Gi-Oh! Master Duel | 32,340 | 0.92% | 16 | 2:23:46 |
| 22. | F-Zero Climax | 31,725 | 0.90% | 7 | 1:59:56 |
| 23. | F-Zero: Maximum Velocity | 29,632 | 0.84% | 5 | 1:14:39 |
| 24. | Yu-Gi-Oh! The Duelists of the Roses | 27,915 | 0.80% | 18 | 4:58:19 |
| 25. | Battalion Wars | 27,862 | 0.79% | 19 | 5:37:03 |
| 26. | Fire Emblem: The Sacred Stones | 27,296 | 0.78% | 43 | 3:01:16:13 |
| 27. | Pokémon Snap | 26,600 | 0.76% | 7 | 45:31 |
| 28. | The Legend of Zelda | 25,124 | 0.72% | 3 | 1:01:48 |
| 29. | Puyo Puyo 2 | 25,088 | 0.71% | 3 | 27:25 |
| 30. | Game Boy Wars | 23,279 | 0.66% | 4 | 43:34 |
| 31. | Mega Man Network Transmission | 23,126 | 0.66% | 29 | 4:01:14 |
| 32. | Super Mario War | 23,121 | 0.66% | 1 | 9:50 |
| 33. | New Super Mario Bros. Wii | 22,006 | 0.63% | 2 | 6:07 |
| 34. | Mega Man X6 | 21,733 | 0.62% | 13 | 4:38:02 |
| 35. | Mega Man Battle Network 4 | 21,032 | 0.60% | 16 | 9:08:54 |
| 36. | BS Zelda no Densetsu: Inishie no Sekiban | 17,578 | 0.50% | 7 | 3:34:28 |
| 37. | Advance Wars: Days of Ruin | 16,450 | 0.47% | 26 | 16:05:51 |
| 38. | Fire Emblem: Genealogy of the Holy War | 13,311 | 0.38% | 2 | 19:10 |
| 39. | The Elder Scrolls II: Daggerfall | 12,639 | 0.36% | 20 | 10:08:10 |
| 40. | Apollo Justice: Ace Attorney | 12,125 | 0.35% | 4 | 1:58:36 |
| 41. | Super Smash Bros. Brawl | 11,401 | 0.32% | 22 | 1:39:32 |
| 42. | Kirby's Dream Course | 11,335 | 0.32% | 20 | 5:13:44 |
| 43. | Pac-Man World | 11,313 | 0.32% | 1 | 4:33 |
| 44. | F-Zero AX | 10,755 | 0.31% | 1 | 25:46 |
| 45. | Harry Potter and the Philosopher's Stone | 10,621 | 0.30% | 31 | 5:02:41 |
| 46. | Yu-Gi-Oh! Capsule Monster Coliseum | 10,434 | 0.30% | 5 | 3:43:56 |
| 47. | Yu-Gi-Oh! Reshef of Destruction | 9,660 | 0.28% | 1 | 2:33 |
| 48. | The Legend of Zelda: Ocarina of Time | 9,611 | 0.27% | 58 | 21:12:10 |
| 49. | Yu-Gi-Oh! The Sacred Cards | 8,598 | 0.24% | 14 | 3:50:50 |
| 50. | Professor Layton vs. Phoenix Wright: Ace Attorney | 7,967 | 0.23% | 1 | 39:27 |
| 51. | Mario Bros. | 7,816 | 0.22% | 1 | 9:59 |
| 52. | The Legend of Zelda: Link's Awakening | 7,362 | 0.21% | 7 | 3:37:36 |
| 53. | Super Mario World | 6,496 | 0.19% | 3 | 27:24 |
| 54. | Dr. Mario Online Rx | 6,328 | 0.18% | 1 | 4:36 |
| 55. | The Legend of Zelda: A Link to the Past | 6,116 | 0.17% | 14 | 5:09:04 |
| 56. | RPG Maker XP | 6,096 | 0.17% | 3 | 55:11 |
| 57. | The Elder Scrolls: Arena | 5,967 | 0.17% | 10 | 5:01:34 |
| 58. | Final Fantasy VIII | 5,940 | 0.17% | 2 | 21:52 |
| 59. | Final Fantasy XI | 5,638 | 0.16% | 10 | 1:04:20 |
| 60. | The Elder Scrolls IV: Oblivion | 5,513 | 0.16% | 6 | 20:58 |
| 61. | Final Fantasy X | 5,369 | 0.15% | 13 | 1:27:50 |
| 62. | Hoshi Wo Miru Hito | 5,245 | 0.15% | 1 | 18:49 |
| 63. | Castlevania | 4,770 | 0.14% | 3 | 43:01 |
| 64. | Yu-Gi-Oh! True Duel Monsters: Sealed Memories | 4,391 | 0.13% | 1 | 3:07 |
| 65. | Final Fantasy | 4,238 | 0.12% | 2 | 11:55 |
| 66. | Soulcalibur III | 4,143 | 0.12% | 2 | 12:26 |
| 67. | Mega Man | 4,073 | 0.12% | 4 | 1:01:09 |
| 68. | The Great Ace Attorney: Adventures | 4,015 | 0.11% | 9 | 4:06:45 |
| 69. | Mega Man Legends | 3,911 | 0.11% | 18 | 6:32:46 |
| 70. | Super Smash Bros. Melee | 3,774 | 0.11% | 2 | 15:49 |
| 71. | The Embodiment of Scarlet Devil | 3,620 | 0.10% | 6 | 47:36 |
| 72. | SRPG Studio | 3,611 | 0.10% | 5 | 1:41:48 |
| 73. | Mega Man Battle Network 2 | 3,534 | 0.10% | 5 | 36:37 |
| 74. | RPG Maker 2003 | 3,516 | 0.10% | 1 | 12:28 |
| 75. | Mega Man 9 | 3,499 | 0.10% | 1 | 4:13 |
| 76. | Tetris | 2,958 | 0.08% | 5 | 15:59 |
| 77. | Tetris Attack | 2,908 | 0.08% | 2 | 21:03 |
| 78. | Yu-Gi-Oh! Ultimate Masters: World Championship Tournament 2006 | 2,890 | 0.08% | 1 | 4:34 |
| 79. | Super Paper Mario | 2,847 | 0.08% | 1 | 3:24 |
| 80. | Mega Man X: Command Mission | 2,416 | 0.07% | 1 | 6:20 |
| 81. | Mega Man 2 | 2,374 | 0.07% | 4 | 1:33:17 |
| 82. | Fire Emblem: Shadow Dragon and the Blade of Light | 2,310 | 0.07% | 5 | 8:26:58 |
| 83. | The Grandmaster | 2,285 | 0.07% | 5 | 43:38 |
| 84. | Pokémon Gold and Silver | 2,269 | 0.06% | 12 | 6:49:52 |
| 85. | Digimon Rumble Arena | 2,263 | 0.06% | 2 | 20:43 |
| 86. | Harry Potter and the Chamber of Secrets | 2,211 | 0.06% | 6 | 1:02:13 |
| 87. | Mega Man 4 | 2,122 | 0.06% | 2 | 1:16:49 |
| 88. | Line Rider | 2,097 | 0.06% | 4 | 11:36 |
| 89. | Castlevania: Harmony of Despair | 2,040 | 0.06% | 2 | 18:31 |
| 90. | Tetris: The Grand Master | 1,936 | 0.06% | 1 | 12:33 |
| 91. | Mega Man Battle Network 3 | 1,779 | 0.05% | 4 | 4:31:39 |
| 92. | Ember | 1,556 | 0.04% | 4 | 10:18 |
| 93. | GoldenEye 007 | 1,537 | 0.04% | 1 | 9:51 |
| 94. | Puyo Pop Fever | 1,503 | 0.04% | 1 | 7:06 |
| 95. | Namco Museum Vol. 3 | 1,453 | 0.04% | 1 | 9:01 |
| 96. | Dr. Mario | 1,391 | 0.04% | 2 | 12:35 |
| 97. | Soulcalibur IV | 1,278 | 0.04% | 1 | 3:02 |
| 98. | Puyo Puyo Sun | 1,269 | 0.04% | 1 | 2:35 |
| 99. | Super Mario RPG | 1,227 | 0.03% | 13 | 9:48:15 |
| 100. | The Misadventures of Tron Bonne | 1,213 | 0.03% | 1 | 9:37 |
