I don't particularly like writing antagonists. I guess because of that, they don't often figure among my favorite characters. That my stories don't often have the "recommended" protag/antagonist dynamic* makes it a doubly hard-to-answer question.
I guess I would say Behrouz of To Be Undone. He is willing to do pretty reprehensible things in order to bring about a change that is for the ultimate good of all. I think a lot of people in life go wrong in this way. They have good intentions, but they become monsters in trying to bring about the change they desire. It makes him comprehensible to me in ways that other antagonists are not (frex, Valsidire in The Traveler's Daughter, who acts out of hunger for power).
* I'm referring to the writing advice that states that the antagonist stands directly in the protag's way and the antagonist deliberately and step-by-step thwarts the protag's advance or achievement.