| 1. | Pokémon HeartGold and SoulSilver | 510,066 | 16.56% | 53 | 23:06:02 |
| 2. | Star Fox 64 | 162,353 | 5.27% | 18 | 3:01:04 |
| 3. | Drakengard 2 | 117,745 | 3.82% | 21 | 13:16:18 |
| 4. | Pokémon FireRed and LeafGreen | 111,281 | 3.61% | 32 | 13:34:34 |
| 5. | Dragon Quest | 93,579 | 3.04% | 190 | 5:00:21:47 |
| 6. | Chrono Cross | 91,822 | 2.98% | 57 | 1:02:28:52 |
| 7. | Donkey Kong 64 | 90,739 | 2.95% | 92 | 1:04:55:19 |
| 8. | Super Chinese World 2 | 88,985 | 2.89% | 14 | 3:30:55 |
| 9. | Monster Hunter | 85,179 | 2.77% | 20 | 5:57:01 |
| 10. | Suikoden III | 82,479 | 2.68% | 40 | 1:03:51:56 |
| 11. | Treasure of the Rudras | 70,002 | 2.27% | 56 | 22:05:02 |
| 12. | The Legend of Zelda: A Link to the Past | 61,693 | 2.00% | 22 | 6:53:09 |
| 13. | Undertale | 46,093 | 1.50% | 23 | 14:09:45 |
| 14. | The Legend of Zelda: Ocarina of Time | 42,499 | 1.38% | 34 | 18:08:14 |
| 15. | Vandal Hearts | 42,180 | 1.37% | 40 | 20:42:16 |
| 16. | Dragon Quest Monsters | 36,104 | 1.17% | 39 | 12:15:25 |
| 17. | Final Fantasy VII | 31,197 | 1.01% | 43 | 22:04:52 |
| 18. | Mystery Dungeon: Shiren the Wanderer | 29,792 | 0.97% | 110 | 2:01:11:00 |
| 19. | Lufia II: Rise of the Sinistrals | 26,312 | 0.85% | 29 | 17:44:17 |
| 20. | Bomberman 64 | 26,308 | 0.85% | 16 | 3:47:21 |
| 21. | Tales of Destiny | 24,590 | 0.80% | 34 | 23:02:09 |
| 22. | 007: Nightfire | 24,390 | 0.79% | 5 | 57:12 |
| 23. | Super Mario All-Stars | 24,099 | 0.78% | 34 | 7:04:30 |
| 24. | Final Fantasy IV: The After Years | 23,853 | 0.77% | 26 | 11:21:24 |
| 25. | Final Fantasy V | 22,418 | 0.73% | 33 | 15:21:18 |
| 26. | Tales of Destiny 2 | 22,182 | 0.72% | 28 | 22:52:16 |
| 27. | I Wanna Be the Guy | 21,170 | 0.69% | 27 | 5:45:27 |
| 28. | Star Fox: Assault | 20,851 | 0.68% | 10 | 3:33:40 |
| 29. | Way of the Samurai 2 | 20,110 | 0.65% | 25 | 11:45:54 |
| 30. | Chocobo's Dungeon 2 | 16,530 | 0.54% | 18 | 11:42:23 |
| 31. | Earthbound | 14,999 | 0.49% | 41 | 15:07:26 |
| 32. | Pokémon Ruby and Sapphire | 14,824 | 0.48% | 33 | 16:20:42 |
| 33. | Tales of Phantasia | 14,737 | 0.48% | 25 | 13:30:05 |
| 34. | Final Fantasy IX | 13,828 | 0.45% | 36 | 23:54:22 |
| 35. | Pokémon Crystal | 13,347 | 0.43% | 32 | 13:51:51 |
| 36. | Mario Kart 64 | 12,678 | 0.41% | 5 | 1:53:49 |
| 37. | Secret of Mana | 12,494 | 0.41% | 23 | 10:00:08 |
| 38. | Final Fantasy XIII | 12,242 | 0.40% | 5 | 2:09:51 |
| 39. | Romancing SaGa | 12,153 | 0.39% | 28 | 9:51:18 |
| 40. | Revelations: Persona | 12,122 | 0.39% | 21 | 10:51:52 |
| 41. | Soul Blazer | 12,008 | 0.39% | 19 | 6:23:28 |
| 42. | Xardion | 11,495 | 0.37% | 6 | 1:15:32 |
| 43. | Diddy Kong Racing | 11,458 | 0.37% | 16 | 3:12:51 |
| 44. | Trials of Mana | 11,414 | 0.37% | 26 | 13:55:42 |
| 45. | Chrono Trigger | 11,313 | 0.37% | 26 | 14:01:06 |
| 46. | The Legend of Zelda: Link's Awakening | 10,888 | 0.35% | 52 | 16:30:57 |
| 47. | Mother 3 | 10,619 | 0.34% | 40 | 17:09:30 |
| 48. | Clock Tower | 10,433 | 0.34% | 9 | 3:43:06 |
| 49. | Illusion of Gaia | 10,065 | 0.33% | 19 | 7:54:33 |
| 50. | GoldenEye 007 | 9,678 | 0.31% | 26 | 7:24:03 |
| 51. | Terranigma | 9,335 | 0.30% | 23 | 11:17:32 |
| 52. | Super Mario RPG | 9,323 | 0.30% | 12 | 6:52:46 |
| 53. | Super Mario 64 | 9,048 | 0.29% | 22 | 5:30:49 |
| 54. | Final Fantasy X | 8,964 | 0.29% | 47 | 1:11:45:06 |
| 55. | Tales of Eternia | 8,903 | 0.29% | 47 | 22:48:36 |
| 56. | Doraemon 2: Nobita no Toys Land Daibouken | 8,577 | 0.28% | 7 | 2:06:45 |
| 57. | Breath of Fire II | 8,567 | 0.28% | 13 | 6:59:26 |
| 58. | Final Fantasy: The 4 Heroes of Light | 8,136 | 0.26% | 9 | 2:59:20 |
| 59. | Final Fantasy Legend II | 8,053 | 0.26% | 26 | 9:05:45 |
| 60. | Monster Hunter Freedom Unite | 7,702 | 0.25% | 48 | 1:11:35:17 |
| 61. | Daikaijuu Monogatari II | 7,676 | 0.25% | 32 | 18:09:52 |
| 62. | Torneko: The Last Hope | 7,573 | 0.25% | 48 | 1:05:48:39 |
| 63. | Breath of Fire | 7,490 | 0.24% | 13 | 7:10:51 |
| 64. | Star Fox Adventures | 7,048 | 0.23% | 12 | 8:35:44 |
| 65. | The Legend of Zelda: Oracle of Ages | 6,813 | 0.22% | 28 | 8:49:12 |
| 66. | Dragon Quest V: Hand of the Heavenly Bride | 6,783 | 0.22% | 27 | 15:27:10 |
| 67. | Custom Robo V2 | 6,726 | 0.22% | 31 | 11:06:39 |
| 68. | Mega Man X4 | 6,720 | 0.22% | 17 | 4:03:47 |
| 69. | The Final Fantasy Legend | 6,691 | 0.22% | 18 | 7:28:56 |
| 70. | Tokimeki Memorial | 6,532 | 0.21% | 23 | 9:10:35 |
| 71. | Mega Man X3 | 6,284 | 0.20% | 13 | 3:05:25 |
| 72. | Tales of Legendia | 5,955 | 0.19% | 29 | 1:09:08:07 |
| 73. | Gakkou de atta Kowai Hanashi | 5,931 | 0.19% | 19 | 6:48:52 |
| 74. | Monster Hunter Portable 3rd | 5,750 | 0.19% | 32 | 23:23:37 |
| 75. | Mega Man X5 | 5,710 | 0.19% | 12 | 3:21:40 |
| 76. | Final Fantasy Tactics | 5,664 | 0.18% | 44 | 21:58:19 |
| 77. | Dragon Ball Z: Super Butōden | 5,440 | 0.18% | 7 | 1:17:20 |
| 78. | P.T. | 5,126 | 0.17% | 3 | 43:21 |
| 79. | Donkey Kong Country 2 | 4,837 | 0.16% | 18 | 4:35:24 |
| 80. | ActRaiser | 4,781 | 0.16% | 8 | 3:00:35 |
| 81. | Dragon Quest Monsters: Caravan Heart | 4,778 | 0.16% | 28 | 11:32:01 |
| 82. | Star Fox | 4,709 | 0.15% | 9 | 3:07:51 |
| 83. | Wonder Project J | 4,520 | 0.15% | 15 | 4:40:08 |
| 84. | Galaxian | 4,517 | 0.15% | 61 | 16:23:44 |
| 85. | Final Fantasy | 4,464 | 0.14% | 6 | 2:06:17 |
| 86. | Ico | 4,442 | 0.14% | 14 | 5:18:24 |
| 87. | Mega Man X2 | 4,425 | 0.14% | 8 | 1:38:29 |
| 88. | Dark Cloud | 4,410 | 0.14% | 13 | 5:42:45 |
| 89. | Mega Man 4 | 4,314 | 0.14% | 10 | 1:31:57 |
| 90. | Devil May Cry 3 | 4,300 | 0.14% | 15 | 4:41:56 |
| 91. | Tales of Rebirth | 3,986 | 0.13% | 15 | 7:51:58 |
| 92. | Doraemon Kimi to Pet no Monogatari | 3,960 | 0.13% | 10 | 3:53:06 |
| 93. | Mega Man 3 | 3,755 | 0.12% | 8 | 1:06:20 |
| 94. | Mega Man 2 | 3,733 | 0.12% | 7 | 1:00:14 |
| 95. | Silent Hill | 3,502 | 0.11% | 22 | 9:43:25 |
| 96. | Kirby's Adventure | 3,476 | 0.11% | 9 | 2:47:30 |
| 97. | Mega Man 6 | 3,468 | 0.11% | 10 | 1:53:00 |
| 98. | Xenogears | 3,424 | 0.11% | 38 | 1:04:57:29 |
| 99. | Mega Man | 3,407 | 0.11% | 7 | 2:31:05 |
| 100. | Super Ghouls 'n Ghosts | 3,386 | 0.11% | 8 | 1:47:26 |
