I got to say Wind Waker. I think its flawless. It took the advancements of OoT and made it perfect. It had an amazing soundtrack, so much exploring. Some people complained about the graphics, but you can't lie, the cartoon style caught everyone's eye. The graphics were also the smoothest of all of the games, it didn't look pixelated at all, where TP did.
For second I would have to say probably OoS only because I spent so much time playing it when I was little.