My favorite would be OoT, even though it has lots of things that annoy me.
Second is Minish cap, but i am nowhere near the end. It's just that it is the best 2d game for me and i prefer 2d anyday (and those minish woods are beyond beatiful).
Third is Majora's Mask, i like the story and the atmosphere, but i HATE the time limit, i just HATE it like no other thing.
And i get more and more dissapointed in AlttP, first i thought i would love it most, but then it got ridiculously hard and frustrating, especially when i was trying to reach the Misery Mire. How the hay was i supposed to know or guess the way to get that Travelling duck? Or that i needed that magic medallion to enter the dungeon itself? Or where to seek for the medallion? Without the internet i would've gave up long ago, because those "puzzles" give no frikkin clue about what to do. I AM PISSED!!!