I went for Phantasy Star IV. Easily one of the best games of the generation and the best RPG ever released until that point. It's certainly a great end to the original story, but I do wonder what could have been if they made Phantasy Star V with a new plot on the Saturn...
Doom probably deserves to win overall, the quality and the impact are both there in spades.
People are only voting Link's Awakening because its Zelda.
And finally, I'll give shout-outs to Secret of Mana and Gunstar Heroes. Both excellent too.