As far as I'm concerned, Legend of Zelda should beat out any game on the list. I'll be honest, Chrono and the Metal Gear series are probably my top games. But as far the influence, the pervasiveness, and the sheer awesomeness? Zelda wins every time. The sad fact is that Mario is great, but the gameplay never significantly expands. Or when it did, it imbibed basically Zelda elements. Zelda has grown and changed over the years, as well as influencing all games.
Mario is great, but I think Zelda is better. Game Informer ranks the original as the best game of all time out of two hundred others.
Anyway, that's my rant for the night on the subject.