Mine would be Slade or Deathstroke from the Teen Titans. Admittedly, I only like the cartoon version of him, but the comic book versions are not bad either I guess.
https://www.youtube.com/watch?v=DCg3yAM7ZC4
He is the guy wearing metal (he shows up later in the video) and so yeah. If you have not seen the show then you probably should because it is great!
In Marvel its green goblin (but not the amazing spider-man 2 version) and in DC its definitely reverse flash (thawne)
Xox
I'm going to be a little weird and say my favorite super-villain is minor side character Accord from the web serial Worm. ;)
He's a super-villain with some OCD like tendencies whose super power is (as far as I can tell) the ability to understand complex systems in an intuitive way which lets him "improve" them to his liking. Basically he has a very focused sort of super intelligence.
His backstory is that after he got his powers he drew up plans to end world hunger and dependence on non-renewable energy, but no one would listen to him. He got so fed up with things that he turned to villainy in order to make things change, lol.
Too bad he's barely in the story and he (rot13)trgf xvyyrq bss cerggl rneyl, but he's pretty interesting I think.
Has to be The Joker, for me.
Harley Quinn. She almost killed Batman, but the Joker stopped her. What is up with that?
It is not because of the Suicide Squad movie. I read the comics and that was my happy place. I wanted to be here and meet my own Poison Ivy.