So here's some games that didn't make my list but should still be mentioned as some of the greats.
Age of Empires, Alleyway, Anno 1404 (Dawn of Discovery), Bioshock, Blast Corps, Call of Duty 2, Crash Bandicoot 2: Cortex Strikes Back, Donkey Kong Country, Dynamite Cop, Empire: Total War, Guitar Hero III: Legends of Rock, The Legend of Zelda NES, The Legend of Zelda: Skyward Sword, Luigi's Mansion, Medieval II: Total War, Missile Command, Populous III The Beginning, SimCity 2000, STAR WARS: Dark Forces, STAR WARS: Jedi Knight - Dark Forces II, STAR WARS: Shadows of the Empire, Super Mario Galaxy 2, Super Street Fighter II Turbo, Tetris, Ultimate Mortal Kombat III, Uncharted: Drake's Fortune, Warcraft III: Reign of Chaos, Wolfenstein 3D.
And whatever other great game I forgot!