There's just...so many good Villains it's hard to choose...
The Joker is just an overall great character in any medium he was in, be it Arkham Asylum, Killing Joke, or the Dark Knight
Just from the stories I've heard, Kefka and Darth Vader seem so...unreasonably badass...One poisoned the town's water so he could walk thru it without being bothered and the other blew up a planet because he could...
Big Brother wasn't a real person but he was the embodiment of an evil government that controlled you, your money, your free time, and, probably more impressive than anything else, your thoughts! One character was THANKFUL that he was arrested by the government because they thought he was going to rebel against them
But I'm surprised that my top pick wasn't mentioned already...probably because people only know him from the movie or the one episode of the Batman cartoon he was in...
Honestly, Batman took some of the best villains from any comic book series down. Be it the Joker, Scarecrow, or Mr. Freeze.
Batman took Spawn to the limit
Batman beat Superman in a god damn fist fight
But for his single, defining moment...I'd choose Bane
He was the only one able to deduce Batman's identity, came up with the perfect plan to take him down, and broke into the Batcave to get Batman's suit. Then when Bruce Wayne comes in, he tosses it at his feet and says "Put it on, shit is going down." And becomes the ONLY man to beat Batman...and he doesn't just beat him
Bane is the man that broke the bat
He, quite literally, breaks Batman