Ocarina of Time, though Majora's Mask and Twilight Princess are VERY close seconds.
OoT just seemed to have the best, most well done settings, the story felt like the classic epic tail, and the gameplay was basic and fun. MM had similar gameplay as OoT but having to constantly use a bunch of transformation masks got annoying after a while. However it gets MAJOR points for the dark creepy ass settings/situations/music. Twilight Princess had the BEST sword play out of any Zelda game, but constant wolf transforming was as annoying as constant mask transforming, it had the probably the grittiest setting on a Zelda game and the best story besides maybe Skyward Sword, so it gets MAJOR points for that. Overall, what each game did better than the other it did REALLY well, but OoT is still my fav(even though all console Zeldas are really equal, these are my 3 favs).
[Edited on 12.25.2012 7:25 PM PST]