I really have to say that Twilight Princess was my favorite, followed closely by Wind Waker and Ocarina of Time. I really like it because it wasn't quite as whimsical and fairy-tale ish. There were very few parts that I really didn't like, and many parts that I absolutely fell in love with. The bosses in Twilight Princess were, without a doubt, the best in the series. Fyrus, while easy, was just so epic to look at, as well as Morpheel. The final fight with gannondorf was just amazing. The music was amazing. My favorite music was Ordon Village, which also leads me to my favorite place. My favorite place to be in any zelda game ever is Ordon Village. It was just great.
There are lots of other things to say about Twilight Princess, but in short, it was a fabulous game that will be hard to top (although I'm not sure where SS will stand).