Some of these are my favorite, but I listed these as the greatest:
Super Metroid
Warcraft III
Super Smash Melee
Zelda II
Super Mario 64
Gran Turismo 3
Diablo II
Final Fantasy II US
Final Fantasy VII
Zelda OOT
Metal Gear Solid
New Super Mario Bros. (DS)
Street Fighter Alpha 2
Killer Instinct Gold
Oracle of Ages & Seasons
Final Fantasy X
Sonic Adventure
King's Quest V
Metroid Prime
Virtua Fighter 2
TMNT 2