I've always deemed Ocarina of Time superior to not only The Wind Waker but any game in the series for it's my ideal template for a Zelda game. Moreover, due to being one of the earlier installments the three dungeon-plot twist-another few dungeons-final boss plot twist hadn't been butchered to death yet.
OoT boasts superb dungeon design especially during the latter half of the game, memorable bosses, a stellar soundtrack with a fully functional instrument intertwined, and quick, easy transportation via Epona and ocarina warping. Several months ago there was a thread asking which system has the most revolutionary Zelda games. The obvious answer: the N64. While current titles continue to manifest the same level of brilliance it was Ocarina of Time and its successor, Majora's Mask, which made great strides forward in design and control. Maneuvering with the analog stick in the 3D plane was efficient and aiming improved with the lock-on feature.
The Wind Waker is by no means an inferior game but it failed to change the way we play as its two console predecessors had done. That said the narrative is easily the most poignant Nintendo has ever produced with colorful, dynamic characters who bring their problems to the forefront during a family ordeal and ultimate quest to rescue a kingdom from a delusional man.