The Smithsonian Amercian Art Museum is holding an exhibit on the The Art of Video Games next year. They ran a vote on which were the best games and came up with a list of 80. There is a PDF here that lists the selected games.
Here is the list of games that were voted the best:
1943: The Battle of Midway
Advanced Dungeons and Dragons
After Burner
Attack of the Mutant Camels
Bioshock
Boom Blox
Brütal Legend
ChuChu Rocket!
Combat®
Desert Commander
Diablo II
Donkey Kong™
DOOM II
Dune II: Battle for Arrakis
Earthworm Jim
Einhander
Fable
Fallout
Fallout 3
Final Fantasy Tactics
Final Fantasy VII
flOw
Flower
Geometry Wars: Retro Evolved 2
Goldeneye 007
Gradius V
Gunstar Heroes
Halo 2
Heavy Rain
Jumpman
Lord of the Rings: Battle for Middle Earth II
Marble Madness
MassEffect 2
Metal Gear Solid
Metal Gear Solid 2: Sons of Liberty
Metroid Prime 2: Echos
Minecraft
Okami
Pac-Man
Panzer Dragoon II: Zwei
Panzer Dragoon Orta
Panzer Dragoon Saga
Phantasy Star
Phantasy Star IV
Pikmin 2
Pitfall II: Lost Caverns
Pitfall!
Portal
Rez
Shadow of Colossus
Shenmue
Sid Meier’s Pirates!
SimCity
SimCity 2000
Sonic Adventure
Space Invaders
Spy vs Spy
Star Fox™
Star Fox™: Assault
Star Strike
Star Trek: Strategic Operations Simulator
StarCraft
Super Mario 64
Super Mario Brothers 3
Super Mario Galaxy 2
Super Mario World
The Bard’s Tale III: Thief of Fate
The Legend of Zelda
The Legend of Zelda: Link to the Past
The Legend of Zelda: Ocarina of Time
The Legend of Zelda: The Wind Walker
The Legend of Zelda: Twilight Princess
Tom Clancy’s Splinter Cell
Tomb Raider
TRON: Maze-Atron
Uncharted 2: Among Thieves
Utopia
Worms Armageddon
Zack & Wiki: Quest for Barbaros’ Treasure
Zaxxon