Without a doubt, Mister Freeze. Note that I'm specifically referring to the animated one written by Paul Dini and voiced by Michael Ansara, NOT the live-action Arnold Schwarzenegger version. I think he's got the best motivation I've ever seen for a villain: "The one good, pure, and decent thing in my world has been ripped away from me; and I no longer care what I have to do or who I happen to hurt in order to bring her back." He lashes out at the world out of grief and rage, unable to face the fact that his wife's death was ultimately his own fault. That's some powerfully emotional tragedy. I absolutely adore his line in the Mister Freeze one-shot that was released around the time of the last Bat-movie, where he says of his abusive childhood: "I knew then that I was destined to live outside humanity, a lonely observer in a world whose warmth would never touch me." (That pretty much sums up my love life...🙁) Later, when we see him meeting Nora, falling in love with her, and being happy for the first time in his life, you get a full sense of what he's lost and you almost forgive him for putting on the refrigerated armor and seeking vengeance.
My second favorite would be Grand Admiral Thrawn from Timothy Zahn's Star Wars novels, Heir to the Empire, Dark Force Rising, and The Last Command. He's like the Hannibal Lecter of the Star Wars universe: So clever, so cunning, and so insightful that he brings half the Galaxy to its knees without leaving his command chair. He out-thinks and out-maneuvers the heroes at every turn even though he never even meets them face to face. Unlike all the villains in the Star Wars novels and comics that followed, he didn't need another implausibly big planet-cracking superweapon to top the Death Star, he simply used lost pre-Empire technology like Cloaking Devices and Cloning in breathtakingly new and inventive combinations. Also, he was a much more rounded character than most Star Wars villains due to his love of art, which gave him a class, style, and sophistication sorely lacking in Fett, the Emperor and their ilk. I could easily see him played by Sir Anthony Hopkins, Patrick McGoohan, or Sam Niell in a movie version.
My second favorite would be Grand Admiral Thrawn from Timothy Zahn's Star Wars novels, Heir to the Empire, Dark Force Rising, and The Last Command. He's like the Hannibal Lecter of the Star Wars universe: So clever, so cunning, and so insightful that he brings half the Galaxy to its knees without leaving his command chair. He out-thinks and out-maneuvers the heroes at every turn even though he never even meets them face to face. Unlike all the villains in the Star Wars novels and comics that followed, he didn't need another implausibly big planet-cracking superweapon to top the Death Star, he simply used lost pre-Empire technology like Cloaking Devices and Cloning in breathtakingly new and inventive combinations. Also, he was a much more rounded character than most Star Wars villains due to his love of art, which gave him a class, style, and sophistication sorely lacking in Fett, the Emperor and their ilk. I could easily see him played by Sir Anthony Hopkins, Patrick McGoohan, or Sam Niell in a movie version.