Wind Waker definitely.
ALttP and OoT were awesome and revolutionary and served the series well but WW really pushed the boat out (sorry fot he pun).
OoT and MM made us comfortable in the 3D Zelda scene whereas ALttP served future installments well as a basis, but unlike the 3D titles, the 2D titles have never had that seriously risky push that WW was tot he 3D scene.
WW split the community down the middle, scared everyone to hell when it was first revealed and dared to violently shove the series off of a cliff without the security of a Loftwing to catch it.
But it was pushed into new territory that was enjoyable, eye opening and pushed the series conceptually rather than formulaically.
The sense of discovery came back to Zelda like it had done in LoZ, ALttP and MM before it. Islands in the distance held exciting mystery as you approached. We were able to traverse a world never seen before in gaming, a game navigated mostly by sea. No other game had done it as well as Wind Waker did and no game (in my opinion) has since.
It was a risk, it looked weird as hell and the idea of nautical travel had people morbidly curious but it all worked out. WW is my favourite video game of all time, not just my favourite Zelda game. I do think that most people cant look behind what the game looks like, and I can understand that. But WW is wonderfully constructed, well put together game that refined and introduced a lot of fresh exciting potential into the series.
Thanks to WW we never know what to expect with future installments of the Zelda series.
I truly think that Wind Waker did the series justice in more than just function, it helped flesh out the series to what it is at its core; a series of discovery and adventure. WW is a Zelda game with its heart on its sleeve. It may not be a traditional land-based Zelda but I think, as far as what the Zelda series stands for, WW is the one game that has truly done the series justice