For me I'd have to throw in these on the basis of outstanding gameplay, storyline, technical achievement, pure fun or replay value:

Elite
Ultima IV
Dungeon Master
Alternate Reality
Doom / Doom 2
Monkey Island / Monkey Island 2
Half-life
Half-life 2
Heroes of Might and Magic (series)
Fallout / Fallout 2
System Shock / System Shock 2
Civilization (all versions)
Medal of Honor: Allied Assault
Guitar Hero / Guitar Hero 2