As a Zelda fan I would really like to vote for A Link to the Past. But no matter how good it is, it is a more or less a refinement of established formula. On the other hand Civilization just stands out so much for doing something completely different in video games sphere (though heavily influenced by boardgames) and basically launching the 4X genre for video games, so honestly, without second thought, that's where my vote goes.
Honorable mention goes to Lemmings on Amiga, and Alien Breed as a great local co-op shooter.
I think in 90s we will see more and more divergence between mainly computer and mainly console gamers, but since this is quite console heavy site, I expect some of the titles that helped (re)define what video games are, that were PC games, not to come on top.