Guys, here is my top 50. It also doesn't give a fuck about historic value, only about what is actually good and stands the test of time (back at the time I updated this list, like a half a year ago!)
1. Earthbound
2. Castlevania: Symphony of the Night
3. Yoshi's Island
4. Zelda: Link to the Past
5. Chrono Trigger
6. Final Fantasy VI
7. Resident Evil 4
8. Planescape Torment
9. F-Zero GX
9. Gran Turismo 4
11. Zelda: Majora's Mask
12. Pikmin 2
13. Metal Gear Solid 3:Snake Eater
14. Metroid Prime
15. Grim Fandango
16. Super Puzzle Fighter II Turbo
17. Disgaea
17. Phantom Brave
19. Fire Emblem
20. Super Mario Bros. 3
21. Virtua Fighter 4:Evo
22. Tetris Attack (or Tetris)
22. Devil May Cry 1
24. Super Metroid
25. Zelda: Ocarina of Time
26. Grand Theft Auto: San Andreas
27. Super Mario RPG
28. ICO
29. Paper Mario
30. Einhänder
31. Deus Ex
32. Winning Eleven 7
33. Street Fighter Alpha 3
34. Devil May Cry 3
35. Return to Castle Wolfenstein
36. Ninja Gaiden
37. Panzer Dragoon Saga
38. Marble Madness
39. Halo 2
40. Half-Life 2
41. Tomb Raider 1
42. Katamari Damacy
43. Secret of Mana
44. Wario Ware
45. Age of Empires II
45. Pong
47. God of War
48. Rise of Nations
49. Beyond Good and Evil
49. Viewtiful Joe
50. Paper Mario: Thousand Year Door