In alphabetical order:
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
Mass Effect 2
Metal Gear Solid
Metal Gear Solid 2: Sons of Liberty
Metroid Prime 2: Echos
Minecraft
Myst
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 Marios Brothers
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
The Secret of Monkey Island
Tom Clancy's Splinter Cell
Tomb Raider
TRON: Maze-Atron
Uncharted 2: Among Thieves
Utopia
World of Warcraft
Worms Armageddon
Zack & Wiki: Quest for Barbaros' Treasure
Zaxxon
via http://kotaku.com/#!5799017/the-smithsonian-has-picked-the-games-of-its-art-of-video-games-exhibit