Majora's Mask is my pick. It's one of the few Zelda games to actually have any emotion, meaningful interactions with townsfolk, and a real sense of threat in the game world (the constant presence of the falling Moon, and the subsequent destruction of Termina that existed beyond just people talking about it). It also has some of my favorite songs in the series, as well as real strides towards actual storytelling in the series (yes, Ocarina started it on console Zelda, but Majora's Mask took it to the next level).
My big problem with Wind Waker is that it feels very artificial to me, with several noticeable missing dungeons and an extreme amount of padding towards the end of the game with the Triforce hunt. The sailing is also neat at the start of the game, but gets very old very fast and could definitely have done with more warp points.