Some appearances of Ganon/dorf were better than others, but The Wind Waker's Ganondorf was definitely his best. He already had tasted defeat after Ocarina of Time, so he's just super down-to-earth and calculated, rather than foolish and cocky. I don't think he underestimated Link in The Wind Waker as much because of that. Plus you got to see a more human side to him right before the final battle, and that was pretty sweet. I did like Ghirahim, too. I liked that you got to regularly interact with him, and watch as his demeanor changed when he learned that you weren't just some harmless kid. Didn't care too much for the writing of Skyward Sword, but Ghirahim was cool.
I liked Yuga as a character; didn't care for him much as a villain. Demise was pretty blah and shallow. Like I think they tried too hard trying to paint this threat, and then he fell short of the imposing figure they tried to create him to be. Though I think Bellum was probably the worst. Like, he had some potential, I guess, but they didn't really tell us anything about him; we literally know nothing about who or what he is or is supposed to be. As far as we know, he isn't even competent and is just a brainless life parasite and the phantoms are just the byproduct of that. Malladus also shares a similar issue. We are given little to no background on him so we really don't know to what extent his establishment as a villain really touches.