It's really kind of subjective based on what's compared between each game. I personally can't choose between Wind Waker and Majora's Mask as my overall favorite, but there are many that I like for other reasons as well. ALL Zelda games have an amazing character cast, so it'd be impossible for me to choose based on that.
Third best would probably have to be TP because of the best partner (in my opinion), playing as a wolf, and the amazing graphics. I can't believe they discarded them for SS's style, honestly. But the motion controls in Skyward Sword were very well done, contrary to Twilight Princess.
I would have to say either Twilight Princess since that was my first Zelda and it got me hooked onto the franchise, or Skyward Sword since I loved the charm of that game and it was just overall really enjoyable. So many awesome games to choose from though.
Wind Waker is my best console game since its so unique from the rest of the series, and I love the exploration, but Majoras Mask is a close second since its a kind of happy/dark feel like all the characters are happy but they will all die in three days if you don't help them, and the game reminds you of this constantly. My favorite portable is links awakening since its so simple but still very adventurous feeling. And it's a good length one for being on the to