I'm going to have to say Ocarina of Time. It was the first big move in to 3D for the game and opened up a huge world to explore. Great story with great gameplay, and all the tools that we got to enjoy from previous games as well as new ones. Expanding the ocarina from A Link to the Past for players to actually play songs was a novel idea; I still to this day remember the notes for most of the songs, and the music was amazing for setting the game's mood.
Ocarina of time, without a doubt. MM wasn't so bad of a game either, but it lacks the special something that made OcT such a worldwide success. I still reverently go through OoT at least onvce every two years and still enjoy it.
I think that "special something" that fallensky is talking about is a feeling of changing the world. Where as in OoT Link makes an impact and grows stronger, in MM you have to reset every 3 days. while Link gets new weapons and tools, the world itself is just about the same, and isn't the hyrule we've grown accustomed to. The way I see it: interesting concept, fun game, but not the same impact as Ocarina of Time.
My favorites would be 1. Ocarina Of Time, and 2. Wind Waker. OOT brought in the 3d graphics really well, also brought in one of the best games even today. Wind Waker was fun, the sailing was boring, but it brought a new sight to TLoZ series, the kiddie graphics, I liked them. OOT would still get an easy 9/10 and WW would get 7.5/10.
