I'm an avid fan of antagonists, so I can think up a few right away.
The Wicked Witch of the West:
--Someone kills your sister then steals your family heirloom, you would be pissed too. The witch was very calm in the situation, considering the alternatives. Despite the fact that this thief and murderer was trying to flee the country with her family's shoes, she gave multiple chances to try and take them without harming Dorothy, or causing more death than necessary. She gave the girl many chances to turn herself in, and even gave Emerald city a chance to hand her in despite the fact that she could have just attacked the city.
Even when she has Dorothy, she is surprisingly civil with her. In fact, despite being named "the wicked", the witch does not kill a single soul in the movie.
Both deaths in the story are caused by Dorothy....
Ivan Drago
Months and years of physical training, diet regulation, high-tech conditioning. He should have won against Rocky without much effort at all.
Syndrome
Sure, hunting down and killing super-heroes is a bad thing, but think about his goals. But can we ever be mad at someone who wanted to give us all rocket-boots?
The Machines (Matrix)
Humans fought them for petty reasons despite them being very reasonable about their rights. Humanity went as far as killing their world just to stop the machines from being equal to them. The machines then harvest Human as energy sources yes, but they are very....humane..about it. Allowing us to live out our lives in our glory-days. They even give humans the chance to regain their glory in the real world, not the bad guys we envision them to be.
Sauron
The ruler of the only mutli-cultural group in all of middle-earth. Who champions industrial revolution and advancement of society. Yes...eeeeevil.