That's a tough one.
Overall, I played Ocarina of Time the most mainly because I find the game to be refreshing every single time I play it. Wind Waker was excellent to become immersed in (I also like that version of Link the most out of any). Majora's Mask had the greatest characters and possibly the greatest story in Zelda history. Twilight Princess had awesome dungeons and excellent bosses. Skyward Sword is everything good about Zelda mixed into one.
Honestly, I can't decide. Let's just say all of the above.
I'm a little ashamed to admit it but I never really completed any of the 2D games, even though I have most of them.