Well, I'll start by saying I don't want to see it done again, but, I'm going with Wind Waker! I loved the solid colours and lack of textures along with the really defined cel-shading style, and the character proportions were so exaggerated and I liked the variety it gave people, but, one thing I adored about Wind Waker's art style were the animations! Specifically facial animations. I thought they worked extremely well, simple and yet they could convey so much emotion and it was cute and quirky and really gave the game some charm. Link especially has never had so much personality, and he didn't even say a word!
And that's why I wasn't the biggest fan of Skyward Sword's art style. I felt like it lost the charm that Wind Waker's cutesy, exaggerated expressions and proportions had. In no way did I dislike Skyward Sword, it was, and still is, a very pretty game, but the lack of that charm I adored so much in Wind Waker means I'll always peg it below.
As for Twilight Princess, and Ocarina of Time, I have no real strong feelings for or against either of them. I felt TP had a problem with a lot of colours getting quite flushed out, especially in the Twilight world, but, they served their purpose, weren't exciting but weren't exactly bad either, and OoT did look pretty good for it's time for sure, so, I can respect it for that. TP didn't exactly break boundaries when it was released. I'd peg both of them below Wind Waker and perhaps Skyward Sword too.
So, as I said, I liked Wind Waker the best but I like Wind Waker being what it is. That art-style should have stayed there, and I hope it doesn't get dregged up again for a console Zelda. I think more Twilight Princess would be the art-style I'd want them to try for a Zelda Wii U, I'd love to see a realistic Zelda made on the powerful(er) Wii U hardware.