Top 100 list, reordered by year

1990, 67, The Secret of Monkey Island

1992, 90, Ultima VII

1993, 32, Day of the Tentacle
1993, 43, Doom

1995, 76, Full Throttle

1996, 52, Tomb Raider (I hope they don't mean the 2013 reboot)
1996, 58, Red Alert
1996, 72, Quake

1997, 25, Age of Empires
1997, 36, Dungeon Keeper
1997, 53, Theme Hospital

1998, 28, Grim Fandango
1998, 61, Half-Life
1998, 81, Starcraft: Brood War

1999, 22, Planescape: Torment
1999, 38, Alpha Centauri
1999, 39, System Shock 2
1999, 44, Quake III
1999, 57, Rollercoaster Tycoon
1999, 68, Freespace 2

2000, 5, Deus Ex
2000, 27, Baldur's Gate 2
2000, 41, Total War: Shogun
2000, 78, Combat Mission: Beyond Overlord

2001, 42, Return to Castle Wolfenstein
2001, 91, Tribes 2

2002, 60, No One Lives Forever 2
2002, 87, Masq
2002, 93, The Elder Scrolls III: Morrowind

2003, 12, EVE Online
2003, 26, SimCity 4
2003, 55, Beyond Good & Evil
2003, 74, Max Payne 2

2004, 3, Half-Life 2
2004, 15, World of Warcraft
2004, 31, Rome: Total War
2004, 59, Unreal Tournament 2004
2004, 89, Vampire: The Masquerade - Bloodlines

2005, 62, F.E.A.R.
2005, 98, Call of Cthulhu: Dark Corners of the Earth

2006, 17, Hitman: Blood Money
2006, 19, Company of Heroes
2006, 50, Flight Sim X
2006, 64, Dwarf Fortress
2006, 73, The Elder Scrolls IV: Oblivion
2006, 75, Galactic Civilizations II
2006, 99, Battle of Britain 2

2007, 4, Team Fortress 2
2007, 7, Bioshock
2007, 14, Portal
2007, 23, Supreme Commander: Forged Alliance
2007, 47, The Witcher
2007, 77, Call of Duty: Modern Warfare
2007, 85, Peggle

2008, 54, Far Cry 2
2008, 63, Fallout 3
2008, 86, Mount & Blade
2008, 100, World of Goo

2009, 9, Left 4 Dead 2
2009, 13, ARMA 2
2009, 24, Dragon Age: Origins
2009, 33, Spelunky
2009, 34, League of Legends
2009, 56, The Sims 3
2009, 65, Batman: Arkham Asylum
2009, 69, Empire: Total War
2009, 71, STALKER: Call of Pripyat
2009, 80, Torchlight
2009, 88, Assassin's Creed II
2009, 94, Plants vs. Zombies

2010, 2, Mass Effect 2
2010, 10, Starcraft II
2010, 20, Civilization V
2010, 84, Super Meat Boy

2011, 1, The Elder Scrolls V: Skyrim
2011, 8, Minecraft (first public release 2009)
2011, 11, Deus Ex: Human Revolution
2011, 29, Battlefield 3
2011, 30, The Witcher 2
2011, 46, Dark Souls
2011, 48, Portal 2
2011, 83, Sins of a Solar Empire: Rebellion
2011, 97, OMSI

2012, 6, XCOM: Enemy Unknown
2012, 18, FTL
2012, 35, Planetside 2
2012, 37, Counter-Strike: Global Offensive
2012, 45, DayZ
2012, 40, Dishonored
2012, 49, FIFA 13
2012, 51, Crusader Kings 2
2012, 70, Tribes: Ascend
2012, 79, Borderlands 2
2012, 82, The Walking Dead: Season 1
2012, 92, Thirty Flights of Loving
2012, 95, Hotline Miami
2012, 96, Diablo III

2013, 16, Bioshock Infinite
2013, 21, DOTA 2
2013, 66, Rising Storm