I want to do this as well! It's important to notice that every single one of these games would probably get a 5/5 from me, or at least 4.8/5. So basically, there are loads of fantastic games that just didn't make the cut. Man, this was hard! But I think I'm happy with the list.
1. Super Mario World
2. Super Castlevania 4
3. Phantasy Star 4
4. Secret of Mana
5. Final Fantasy 6
6. The Legend of Zelda: A Link to the Past
7. Shining Force 2
8. Castlevania: Symphony of the Night
9. Super Metroid
10. Shenmue 2
11. Tomba!
12. Suikoden 2
13. Castlevania 3: Dracula's Curse
14. Dragon Quest 8
15. Landstalker
16. Mega Man 2
17. Dragon Quest 5
18. Contra 3
19. The Legend of Zelda: Link's Awakening
20. Klonoa 2
21. Castlevania
22. Duck Tales
23. Suikoden
24. Seiken Densetsu/Final Fantasy Adventure
25. Yakuza 2
26. Alundra
27. Fire Emblem: Awakening
28. The Legend of Zelda: The Minish Cap
29. Final Fantasy 4
30. Kirby's Adventure
31. Klonoa
32. Shenmue
33. Phantasy Star 2
34. Mega Man 3
35. Super Mario Bros 3
36. Gabriel Knight: Sins of the Fathers
37. Tetris
38. Axelay
39. Yakuza 4
40. Suikoden 5
41. Strider 2
42. Tomba! 2
43. Shining Force
44. Okami
45. Valkyria Chronicles
46. Castlevania: Dawn of Sorrow
47. Super Mario Galaxy
48. Metroid: Zero Mission
49. Shadow of the Colossus
50. Folklore
51. Yakuza 3
52. Jeanne D'Arc
53. The Legend of Zelda: Twilight Princess
54. Castle of Illusion starring Mickey Mouse
55. Sim City
56. Persona 4
57. Kirby Super Star
58. The Elder Scrolls: Morrowind
59. Super Mario World 2: Yoshi's Island
60. Final Fight
61. Shinobi (PS2)
62. Ni No Kuni
63. Suikoden 3
64. Mega Man X
65. Castlevania: Order of Ecclesia
66. Chip'n Dale: Rescue Rangers
67. Metroid Prime
68. King's Quest 6
69. Kirby's Dream Land
70. Batman: Arkham Asylum
71. ICO
72. Quackshot
73. Dragon Quest 4
74. Street Fighter 2 Turbo
75. 999: Nine Hours, Nine Persons, Nine Doors
76. Professor Layton & the Lost Future
77. Super Mario Bros
78. Castlevania Bloodlines
79. Ninja Gaiden
80. Yakuza
81. Legend of Heroes: Trails in the Sky
82. Punch Out!!
83. Dragon Quest 9
84. Sonic 2
85. Super Mario Kart
86. Nier
87. Bubble Bobble
88. The Legend of Zelda: Oracle of Ages
89. Super Mario 64
90. Castlevania: Aria of Sorrow
91. Kirby's Epic Yarn
92. Virtue's Last Reward
93. Castlevania: Rondo of Blood
94. Dark Souls
95. Xenoblade Chronicles
96. Eternal Sonata
97. Bayonetta
98. Resident Evil 4
99. The Legendary Starfy
100. Mega Man