It's Wind Waker for me.
Even with the HD remake, it's still the lesser game to the other console games. I know the NES games aren't much too look at, but they gave me a better feeling when I played them. Partly because of the challenge, partly because of the immersion. I was genuinly proud of myself when I finally after all those years completed Adventure of Link. A true accomplishment in my gaming carreer. Actually, I'd like to know how many of those in the poll voting for Zelda II actually played it. Every console Zelda gave me a feeling similar to that, but I never really cared for Wind Waker. Not even when I had completed it for the very first time back in 2003. That's why I must vote for Wind Waker.
The biggest gripe remain the dungeons. They're laughable compared to those in the other console games. Even those in the first two Zeldas. The Tower of the Gods, to me easily the best dungeon of the game, is at least two floors too short and what's accomplished in the dungeon is done better in Twilight Princess's Temple of Time. The HD remake does make me like the game more than I did though. Wind Waker a spot in my favourites-list by overtaking Spirit Tracks.