Well. That depends. I like bits and pieces of style from different games. It also depends on the atmosphere of the game, so I have to take that into consideration. For example I love the colour pallet of Majora's Mask. It has a lot of nice reds, purples, and oranges and other very vibrant yet odd colours, mixed with the black and green it works out really well and fits the atmosphere of the game perfectly.
However, Twilight Princess' colour pallet works really well with it's atmosphere. It has the drab grays, pukish yellows, and pitch blacks mixed with streaks of red. The graphical style and proportions of the game also fit really well into the atmosphere. The same can be said about Wind Waker.
So I don't really have a clear cut favourite, as different things work with different games that have different atmospheres.