Wind Waker, no question
Majora's a close second, but nothing quite compares to WW in my mind, the sailing made the whole world feel really big and open, the art style was easily the best in the franchise (or any other game on the GCN for that matter), the gameplay was nicely varied and balanced, the characters where truthfully memorable, it has one of the best soundtracks in the series, and it has some of the most well designed dungeons I've ever seen. It's not just my favorite Zelda game, it's one of my favorite games PERIOD.