This list will take games from 1995-96 on, since I never feel comfortable ranking stuff that came out before I was conscious, gaming-wise. Sorry, Doom 2. You were awesome, I just don't have any points of reference.
100. Crackdown (Realtime Worlds, 2007)
99. Hitman: Blood Money (IO Interactive, 2006)
98. Star Wars: Republic Commando (LucasArts, 2005)
97. Max Payne 2: The Fall of Max Payne (Remedy Entertainment, 2003)
96. Final Fantasy X-2 (Square, 2003)
95. Warcraft III (Blizzard Entertainment, 2002)
94. The Sims (Maxis, 2000)
93. Prey (Human Head Studios, 2006)
92. Fable (Lionhead Studios, 2004)
91. Assassin's Creed II (Ubisoft, 2009)
90. Final Fantasy XIII (Square Enix, 2010)
89. Lost Odyssey (Mistwalker Studios, 2008)
88. Star Wars: Jedi Outcast (Raven Software, 2002)
87. Final Fantasy XII (Square Enix, 2006)
86. Super Smash Bros (HAL Laboratory, 1999)
85. Quake III: Arena (id Software, 1999)
84. Max Payne 3 (Rockstar Games, 2012)
83. Super Mario Sunshine (Nintendo, 2002)
82. Roller Coaster Tycoon (Hasbro Interactive, 1999)
81. DOOM 3 (id Software, 2004)
80. Dragon Age II (BioWare, 2011)
79. Unreal Tournament (Epic Games, 1999)
78. Dead Space (EA Redwood Shores, 2008)
77. Star Wars: Battlefront (LucasArts, 2004)
76. Star Fox 64 (Nintendo, 1997)
75. BioShock 2 (2k Marin, 2010)
74. The Elder Scrolls III: Morrowind (Bethesda, 2002)
73. Team Fortress 2 (Valve, 2007)
72. Half-Life: Opposing Force (Gearbox, 1999)
71. Gears or War 3 (Epic Games, 2011)
70. Dead Space 2 (EA Redwood Shores, 2011)
69. The Legend of Zelda: Twilight Princess (Nintendo, 2006)
68. Super Smash Bros: Brawl (HAL Laboratory, 2008)
67. Star Wars: Jedi Knight (LucasArts, 1997)
66. Grand Theft Auto: Vice City (Rockstar, 2002)
65. Gears or War 2 (Epic Games, 2008)
64. Borderlands 2 (Gearbox, 2012)
63. StarCraft II (Blizzard Entertainment, 2010)
62. Star Wars: Battlefront 2 (LucasArts, 2005)
61. Jade Empire (BioWare, 2005)
60. Max Payne (Remedy Entertainment, 2001)
59. Resident Evil 4 (Capcom, 2005)
58. Metal Gear Solid 2: Sons of Liberty (KCEJ, 2001)
57. World of Warcraft (Blizzard Entertainment, 2004)
56. Gears of War (Epic Games, 2006)
55. The Elder Scrolls IV: Oblivion (Bethesda, 2006
54. System Shock 2 (Irrational Games, 1999)
53. Diablo III (Blizzard Entertainment, 2012)
52. Metroid Prime 2: Echoes (Retro Studios, 2004)
51. Dragon Age: Origins (BioWare, 2009)
50. Perfect Dark (Rare, 2000)
49. Grand Theft Auto III (Rockstar, 2001)
48. Super Mario 64 (Nintendo, 1996)
47. Halo: Reach (Bungie, 2010)
46. Final Fantasy VIII (Square, 1999)
45. XCOM: Enemy Unknown (Firaxis Games, 2012)
44. Half-Life 2: Episode One (Valve, 2006)
43. L.A. Noire (Team Bondi, 2011)
42. The Legend of Zelda: The Wind Waker (Nintendo, 2003)
41. GoldenEye 007 (Rare, 1997)
40. Halo 3: ODST (Bungie, 2009)
39. Final Fantasy IX (Square, 2000)
38. Halo 4 (343 Industries, 2012)
37. Starcraft (Blizzard Entertainment, 1998)
36. Mass Effect (BioWare, 2007)
35. Dishonored (Arkane Studios, 2012)
34. Star Wars: Knights of the Old Republic II (Obsidian, 2004)
33. Fallout: New Vegas (Obsidian, 2010)
32. The Walking Dead (Telltale Games, 2012)
31. Batman: Arkham City (Rocksteady, 2011)
30. Metal Gear Solid (KCEJ, 1998)
29. BioShock (Irrational Games, 2007)
28. The Legend of Zelda: Ocarina of Time (Nintendo, 1998)
27. Shadow of the Colossus (Team Ico, 2005)
26. Half-Life 2: Episode 2 (Valve, 2007)
25. The Legend of Zelda: Majora's Mask (Nintendo, 2000)
24. Halo 3 (Bungie, 2007)
23. The Legend of Zelda: Skyward Sword (Nintendo, 2011)
22. Batman: Arkham Asylym (Rocksteady, 2009)
21. Metal Gear Solid 3: Snake Eater (KCEJ, 2004)
20. Halo 2 (Bungie, 2004)
19. Super Smash Bros: Melee (HAL Laboratory, 2001)
18. Deus Ex: Human Revolution (Eidos Montreal, 2011)
17. Fallout 3 (Bethesda, 2008)
16. BioShock Infinite (Irrational Games, 2013)
15. Final Fantasy VII (Square, 1997)
14. Half-Life (Valve, 1998)
13. Red Dead Redemption (Rockstar, 2010)
12. Diablo II (Blizzard Entertainment, 2000)
11. The Elder Scrolls V: Skyrim (Bethesda, 2011)
10. Grand Theft Auto IV (Rockstar, 2008)
9. Final Fantasy X (Square, 2001)
8. Mass Effect 3 (BioWare, 2012)
7. Metroid Prime (Retro Studios, 2002)
6. Portal 2 (Valve, 2011)
5. Halo: Combat Evolved (Bungie, 2001)
4. Portal (Valve, 2007)
3. Mass Effect 2 (BioWare, 2010)
2. Star Wars: Knights of the Old Republic (BioWare, 2003)
1. Half-Life 2 (Valve, 2004)
Possible Coming Attractions
Grand Theft Auto V
Batman: Arkham Origins
Watch Dogs
Destiny
Metal Gear Solid V: The Phantom Pain
Halo 5
Halo 6
