I'm gonna agree with Lord Jeff and say that Clock King was pretty neat, and desperately needs to be masterminding complex heists that can be completed in under five minutes.
That being said, my favorite Batman villain was and still is Mr. Freeze, starting with the Animated Series incarnation. They took a one-note petty crook with a fancy gimmick from the old comics and turned him into a complex relatable person whose motivations and backstory codified the Anti-Villain and questioned the very nature of morality itself. He was a villain motivated by love and hope to contrast Batman's hero motivated by pain and revenge.
Not bad for a Nineties kid's cartoon. Hell, I think they could do a viable live-action Freeze, Arnold's performance notwithstanding. Just think about this, and I'm gonna throw it out there, ready boys and girls?
Patrick Stewart.