It's different depending on how you ask...
Design-wise: I'd say Skyward Sword Zelda. She seemed like a simple and relatable girl since I first saw her in the trailers, not like a princess, which can actually look kind of off-turning for me. Even though I didn't really have saving her in mind through the whole game, I still found her scenes with Link really appealing. Let's face it: Many guys like her, and I'm a guy.
Development-wise: I go with Tetra here. The discovery of her being a princess was clearly a pretty big deal in Wind Waker's overall storyline, and made for some memorable (and strangely reminiscent of OoT, in my opinion) scenes.
Memorable moment-wise (wow, that sounds pretty weird...): OoT Zelda, just for the shot at the end of the credits.