Seconding Bruce Dern in The Cowboys. One of my favorite John Wayne movies, and a total sleaze of a villain.
I really like villains who just look like regular guys, because the craziest people often do. Check out Joseph Cotton in "Shadow of a Doubt" (also by Hitchcock). I'll put Delores Umbridge in that category, too. She really looks harmless at first.
Current favorite is Loki from the Thor and Avengers movies. He's a rather sympathetic villain, even if he is a major stinker at times.