Man, there are so many of them, so I'll list here the ones I can think of right off the bat:
Tai Lung, from Kung Fu Panda- When I took my little cousin to watch this movie, I admit I went in with zero expectations. I was not disappointed, and even today refuse to watch the sequel. And yet in my dislike of it, I never expected a character like Tai Lung. He was a great character on every level, but I will say now, I do not see him as a villain. Antagonist, yes, but not a villain. His story's compelling, he's very sympathetic, Ian McShane nails the role, and he has a lot of potential to become a far deeper character than he already is. That is, if the writers of the franchise actually care, because they shamefully turned him into a complete joke in the final part of the movie. We'll see how this goes, but for now, he is to me the one bright spot in what I consider a horrible franchise.
The Joker from Batman: TAS- Sure, there are many versions of the Joker out there, but Mark Hamill's is to me the big stand-out, and to me, the best Joker.
Xanatos and Demona, from Gargoyles- A good case of when the villains totally overshadow the heroes. Demona is a very interesting character in every level, and Xanatos just oozes charm, smarts, excellent one-liners and also has depth all his own. That and their voice actors totally work to give them that extra oomph that makes them all the better.
The Misfits, from Jem- Sure, they may be quite reckless, but they're overall more fun that Jem and the Holograms, and their songs are catchier.
Yzma and Kronk, from Emperor's New Groove- Far more hilarious than the heroes, their entire chemistry is comedic gold.
Don Karnage and Shere Khan, from Tale Spin- Well, Karnage does have his nice moments and Shere Khan is not all-out villainous either. Anyway, here's another example of a franchise I hate, but will watch because of certain characters. Karnage is flat-out hilarious, whoever wrote his lines is one talented person, and Jim Cummings was perfect for the role. Shere Khan just oozes cool and sophisticated with a very dangerous aura to him that he doesn't need to go all-out to display, you just feel it. Plus he's voiced by Tony Jay, that's a win right there.