An obvious one, but
OoT. I mean, the game is a legend in itself. A great storyline, an awesome first 3D Zelda, great level designs, great side quest, it has replayability, some bits were quite scary at parts but also funny and emotional at other times. Basically, what I'm saying is - the game is just great. In my opinion, no game has come close to recapturing the magic like
OoT did. It was a defining point for Zelda and set the benchmark for current games. But
TP is the close second and
ALttP third.