| 1. | Dragon Quest Monsters: Joker 3 | 1,244,686 | 3.91% | 2 | 4:21:18 |
| 2. | Dragon Quest Monsters 2 | 927,042 | 2.91% | 2 | 4:20:02 |
| 3. | Rhythm Tengoku | 856,700 | 2.69% | 1 | 40:52 |
| 4. | Dragon Quest Monsters: Joker 2 | 817,789 | 2.57% | 1 | 2:51:36 |
| 5. | Ape Escape 3 | 683,377 | 2.14% | 3 | 2:52:57 |
| 6. | Dragon Quest V: Hand of the Heavenly Bride | 666,200 | 2.09% | 11 | 1:18:28:14 |
| 7. | Monster Hunter | 560,743 | 1.76% | 3 | 9:22:22 |
| 8. | The Final Fantasy Legend | 547,189 | 1.72% | 3 | 4:39:28 |
| 9. | Dragon Quest | 515,332 | 1.62% | 11 | 17:29:53 |
| 10. | Final Fantasy Legend II | 434,928 | 1.36% | 3 | 7:35:56 |
| 11. | Clock Tower II: The Struggle Within | 372,318 | 1.17% | 1 | 1:38:07 |
| 12. | Resident Evil 7 | 347,935 | 1.09% | 2 | 5:12:04 |
| 13. | GoldenEye 007 | 343,161 | 1.08% | 2 | 4:22:53 |
| 14. | Initial D Extreme Stage | 319,558 | 1.00% | 1 | 1:01:22 |
| 15. | Dragon Quest Monsters: Joker | 315,174 | 0.99% | 1 | 1:29:39 |
| 16. | Dragon Quest III: The Seeds of Salvation | 289,950 | 0.91% | 4 | 9:21:03 |
| 17. | Crash Bandicoot 2: Cortex Strikes Back | 288,191 | 0.90% | 2 | 2:57:16 |
| 18. | Gundam Battle Universe | 267,287 | 0.84% | 1 | 2:13:37 |
| 19. | Star Fox 64 | 264,701 | 0.83% | 4 | 5:23:26 |
| 20. | Donkey Kong Country 2 | 264,115 | 0.83% | 2 | 4:32:11 |
| 21. | Clock Tower | 257,243 | 0.81% | 2 | 3:11:34 |
| 22. | Bomberman 64 | 248,619 | 0.78% | 1 | 2:19:55 |
| 23. | Donkey Kong Country 3 | 238,135 | 0.75% | 3 | 5:31:15 |
| 24. | Etrian Odyssey Nexus | 230,830 | 0.72% | 1 | 3:21:39 |
| 25. | Shin Megami Tensei: Devil Summoner | 222,569 | 0.70% | 1 | 2:38:49 |
| 26. | Romancing SaGa 2 | 222,486 | 0.70% | 6 | 14:39:26 |
| 27. | Labyrinth of Refrain: Coven of Dusk | 185,787 | 0.58% | 1 | 3:50:44 |
| 28. | Atlantis no Nazo | 181,815 | 0.57% | 1 | 19:44 |
| 29. | Super Smash Bros. Ultimate | 181,279 | 0.57% | 2 | 25:09 |
| 30. | Pikmin 2 | 180,813 | 0.57% | 3 | 11:27:23 |
| 31. | Kid Dracula | 173,679 | 0.54% | 1 | 34:25 |
| 32. | Legend of Mana | 173,318 | 0.54% | 2 | 7:13:43 |
| 33. | Dino Crisis 2 | 168,617 | 0.53% | 2 | 4:18:20 |
| 34. | Siren | 165,172 | 0.52% | 1 | 24:12 |
| 35. | Dragon Quest II: Luminaries of the Legendary Line | 162,996 | 0.51% | 6 | 17:25:27 |
| 36. | Parasite Eve | 162,054 | 0.51% | 4 | 18:39:20 |
| 37. | Monster Hunter G | 153,903 | 0.48% | 1 | 1:37:51 |
| 38. | Pokémon Red and Blue | 153,760 | 0.48% | 7 | 14:08:30 |
| 39. | Shin Megami Tensei | 151,846 | 0.48% | 5 | 15:06:58 |
| 40. | MS Saga: A New Dawn | 146,965 | 0.46% | 1 | 4:17:56 |
| 41. | Resident Evil 6 | 146,412 | 0.46% | 8 | 23:54:56 |
| 42. | Boktai 2: Solar Boy Django | 144,472 | 0.45% | 2 | 2:20:26 |
| 43. | Mega Man X6 | 143,402 | 0.45% | 2 | 3:39:13 |
| 44. | Tenchi wo Kurau II | 140,844 | 0.44% | 1 | 1:45:05 |
| 45. | Final Fantasy II | 140,042 | 0.44% | 2 | 7:02:07 |
| 46. | Kagero: Deception II | 139,907 | 0.44% | 1 | 3:24:32 |
| 47. | Bully | 134,088 | 0.42% | 2 | 6:26:56 |
| 48. | Spelunker | 131,629 | 0.41% | 3 | 1:53:42 |
| 49. | Super Mario 64 | 129,518 | 0.41% | 5 | 5:06:24 |
| 50. | Fate/ExtraCCC | 126,554 | 0.40% | 1 | 4:41:52 |
| 51. | Digimon World | 122,366 | 0.38% | 2 | 7:53:00 |
| 52. | Dragon Quest Monsters | 118,157 | 0.37% | 8 | 1:03:04:23 |
| 53. | Fire Emblem Fates | 117,839 | 0.37% | 2 | 5:09:16 |
| 54. | Dragon Ball Z: Kyoushuu! Saiyajin | 113,343 | 0.36% | 1 | 2:03:59 |
| 55. | The Legend of Zelda: Spirit Tracks | 112,618 | 0.35% | 1 | 37:46 |
| 56. | Donkey Kong Country | 111,434 | 0.35% | 1 | 2:00:32 |
| 57. | Tomb Raider | 109,695 | 0.34% | 3 | 13:02:59 |
| 58. | Doraemon 3: Nobita no Machi SOS! | 106,386 | 0.33% | 1 | 3:29:28 |
| 59. | Burger Burger | 99,334 | 0.31% | 2 | 4:54:17 |
| 60. | Dragon Quest X | 98,582 | 0.31% | 1 | 1:06:47 |
| 61. | Fire Emblem Gaiden | 97,860 | 0.31% | 1 | 2:22:33 |
| 62. | Boxer's Road | 92,184 | 0.29% | 1 | 3:20:42 |
| 63. | Dragon Quest IV: Chapters of the Chosen | 89,826 | 0.28% | 6 | 1:00:43:05 |
| 64. | Dragon Ball Z: Super Saiya Densetsu | 89,535 | 0.28% | 2 | 6:56:47 |
| 65. | Super Robot Wars EX | 88,366 | 0.28% | 1 | 3:31:03 |
| 66. | Parasite Eve II | 87,417 | 0.27% | 1 | 5:16:37 |
| 67. | Kaeru no Tame ni Kane wa Naru | 85,982 | 0.27% | 1 | 3:07:46 |
| 68. | Cuphead | 80,403 | 0.25% | 1 | 48:58 |
| 69. | Star Fox: Assault | 78,484 | 0.25% | 1 | 52:14 |
| 70. | Resident Evil 2 | 68,174 | 0.21% | 2 | 3:38:59 |
| 71. | Mario Party | 65,662 | 0.21% | 1 | 44:38 |
| 72. | Disgaea: Hour of Darkness | 65,077 | 0.20% | 1 | 1:46:27 |
| 73. | Clock Tower | 63,701 | 0.20% | 1 | 35:35 |
| 74. | Banjo-Tooie | 63,463 | 0.20% | 3 | 7:20:10 |
| 75. | 4th Super Robot Wars | 62,897 | 0.20% | 1 | 5:58:54 |
| 76. | Dragon Quest VIII: The Journey of the Cursed King | 60,634 | 0.19% | 3 | 11:31:38 |
| 77. | Wizardry | 57,453 | 0.18% | 3 | 7:35:07 |
| 78. | Donkey Kong Country: Tropical Freeze | 54,095 | 0.17% | 1 | 4:23:29 |
| 79. | Fire Emblem: The Binding Blade | 53,693 | 0.17% | 4 | 17:40:24 |
| 80. | Metal Max | 48,735 | 0.15% | 3 | 12:09:52 |
| 81. | Super Mario Bros. 3 | 47,664 | 0.15% | 5 | 9:39:11 |
| 82. | Mega Man | 46,327 | 0.15% | 12 | 20:22:52 |
| 83. | King's Field | 45,761 | 0.14% | 1 | 3:22:44 |
| 84. | Dokapon: Monster Hunter | 45,204 | 0.14% | 1 | 3:02:38 |
| 85. | Valkyrie Profile | 44,718 | 0.14% | 1 | 5:59:48 |
| 86. | Dragon Quest Swords | 44,067 | 0.14% | 2 | 2:45:35 |
| 87. | Shantae: Half-Genie Hero | 43,321 | 0.14% | 1 | 1:22:24 |
| 88. | The Legend of Zelda: Majora's Mask | 43,231 | 0.14% | 2 | 9:29:31 |
| 89. | Chocobo's Dungeon 2 | 42,050 | 0.13% | 5 | 22:29:44 |
| 90. | Wizardry IV: The Return of Werdna | 40,914 | 0.13% | 1 | 4:58:52 |
| 91. | Fire Emblem Awakening | 38,383 | 0.12% | 1 | 2:15:40 |
| 92. | Metal Gear Solid | 37,122 | 0.12% | 6 | 1:01:36:52 |
| 93. | Ao Oni | 36,677 | 0.12% | 6 | 9:43:37 |
| 94. | Final Fantasy III | 36,413 | 0.11% | 2 | 11:27:12 |
| 95. | Dark Souls | 36,329 | 0.11% | 6 | 16:40:56 |
| 96. | Earthbound | 34,329 | 0.11% | 8 | 2:01:47:56 |
| 97. | Cyber Knight | 33,317 | 0.10% | 1 | 2:04:00 |
| 98. | Super Smash Bros. for Nintendo 3DS | 33,075 | 0.10% | 1 | 12:37 |
| 99. | The Legend of Zelda: Oracle of Seasons | 33,036 | 0.10% | 1 | 3:38:07 |
| 100. | The Legend of Zelda: A Link to the Past | 32,762 | 0.10% | 3 | 3:56:47 |
