1. Final Fantasy X (2001)
2. Final Fantasy VII (1997)
3. Dragon Quest III (1988)
4. Dragon Quest VIII (2004)
5. Machi (1998)
6. Final Fantasy IV (1991)
7. Tactics Ogre (1995)
8. Final Fantasy III (1990)
9. Dragon Quest VII (2000)
10. Legend of Zelda: Ocarina of Time (1998)
11. Dragon Quest V (1992)
12. Far East of Eden 2 (1992)
13. Sakura Taisen (1996)
14. Dragn Quest IV (1990)
15. Final Fantasy V (1992)
16. Xenogears (1998)
17. Dragon Quest II (1987)
18. Sakura Taisen III (2002)
19. Kingdom Hearts (2002)
20. Streetfighter II (1992)
21. Super Mario Bros (1985)
22. Final Fantasy VIII (1999)
23. Toki Meki Memorial (1995)
24. Final Fantasy IX (2000)
25. Final Fantasy VI(1994)
26. Metal Gear Solid 3 (2004)
27. Valkyrie Profile (1999)
28. Chrono Trigger (1995)
29. Kingdom Hearts II (2005)
30. Dragon Quest (1986)
31. Zelda 3 (1991)
32. Final Fantasy X-2 (2003)
33. Resident Evil (1996)
34. Dragon Quest VI (1995)
35. F-Zero (1990)
36. Sakura Taisen II (1998)
37. Mother 2 (1994)
38. Mother (1989)
39. Virtua Fighter (1994)
40. Dragon Quest 5 (PS2 remake) 2004
41. Zelda Windwaker (2002)
42. Metal Gear Solid 2 (2001)
43. Animal Crossing (DS) 2005
44. Tales of the Abyss (2005)
45. Ogre Battle (1993)
46. Legend of Zelda (1986)
47. Virtua Fighter 2 (1995)
48. Mysterious Dungeon 2 (1995)
49. Sonic the Hedgehog (1991)
50. Metal Gear Solid (1998)
51. Pokemon Red and Green (1996)
52. Y's 1 and 2 (1989)
53. Romancing Saga (1992)
54. Toke Meke Memorial (PC Engine) 94
55. Super Robot Taisen Alpha (2000)
56. Resident Evil 2 (1998)
57. Tales of Eternia (2000)
58. Digital Devil Story Megami Tensei II (1990)
59. Shin Megami Tensei (1992)
60. Final Fantasy II (1988)
61. Super Mario World (1990)
62. To Heart II (2004)
63. Final Fantasy (1987)
64. Puyo Puyo (1992)
65. Family Stadium Pro Baseball (1986)
66. Wizardry (1987)
67. Hokkaido Murder Mystery (1987)
68. Fire Emblem (1994)
69. Super Mario Kart (1992)
70. Dynasty Warriors 4 (2003)
71. Monster Hunter (2004)
72. Best Play Pro Baseball (1988)
73. Grandia (1997)
74. Resident Evil 4 (GC) 2005
75. Gran Turismo 4 (2004)
76. GTA: Vice City (2004)
77. Super Monaco GP (1990)
78. Torneko Mysterious Dungeon (1993)
79. Tales of Destiny (1997)
80. Streetfighter 2 Turbo (1993)
81. Dynasty Warriors III (2001)
82. Final Fight (1990)
83. Monster Hunter Portable (2005)
84. Final Fantasy Tactics (1997)
85. Minster Hunter G (2005)
86. Mysterious Dungeon 2 (2000)
87. Kung Fu (1985)
88. Toke Meke Memorial (Saturn) (1996)
89. Tales of Destiny II (2002)
90. Kamaitachi No Yoru (1994)
91. Sakura Taisen IV (2002)
92. Tales of Rebirth (2004)
93. Sim City (1991)
94. Saga 2 (1990)
95. Pro Baseball Family Stadium 87
96. Tetris (Gameboy) (1989)
97. Secret of Mana (1993)
98. Gradius (1986)
99. Super Mario Bros III (1988)
100. Resident Evil IV (PS2) 2005
via: http://www.next-gen.biz/features/japan-votes-all-time-top-100