Definitely The Wind Waker. It was my first ever Zelda game, and the world is just so massive and beautiful. The graphics may have been cartoon-y, but I think that only complimented the story, the humor, and the gameplay in such a wonderful and impossible to describe manner.

With a two-way tie in second place, there's Majora's Mask and Twilight Princess. Their stories are so dark and moody, that they really revolutionized the series at their respective times of release. They brought new and innovating ideas to the table, with the mask transformations of Majora's Mask, to exploring the Twilight Realm as Wolf Link in Twilight Princess.

Sure, Ocarina of Time was great, being the first 3D Zelda title, but the games that followed it still live in its shadow half the time, and said games deserve a lot more recognition and praise than what people already give them.