My least favorite is Zelda game is the Minish Cap. I didn't like the gameplay, and the dungeons weren't that fun. The only thing that I enjoyed was Vaati. My second least favorite Zelda game is A Link To The Past. I liked the design and gameplay, and the character design was good. But it was a little bit to hard for me, and I am still not through the first dungeon. I know that alot of people love this game, but I personally think that it was overly hard.
I have two here.
The first would have to be Spirit Tracks. Being so used and comfortable to the medieval fantasy environment of the preceding Zelda games, I find trains a bit...odd.
Pray to God they won't put in motorbikes and spaceships.
The second is The Adventure of Link. It's so hard, it drove me mad!