John “raped and murdered my wife” G is from Memento.
Joe Chill is from Batman.
How about:
Beef Supreme
I have no idea why I’m such a thread killer. I don’t mean to, honestly.
Jame Gumb is from Silence of the Lambs. I’m surprised I’m the first one to get that, since I’m not even a fan of that series… I heard about Jame Gumb because Jay mocks his dance in “Clerks II.”
Someone’s gotta know who Lord Kane and Papa Joe are…
Here’s a few more:
Fred Johnson
Big Daddy
Jack McGee
Ogden Wernstrom
Richard Wilkins
“Don’t make me angry Mr. McGee. You wouldn’t like me when I’m angry.” - Obnoxious reporter from the TV Hulk series.
Ah, I was thinking of The Duke from “Escape from New York,” although his proper title was “The Duke of New York.” Add to that, “number one” if you happen to be the President of the United States of America 
And since when did Vic Mackey become a villian? He’s just as much a hero as Al Sweringen.
My addition, a henchman who got his well deserved comeuppance in a great film noir - Chester.
Richard Wilkins the III was mayor of Sunnydale during season 3 of Buffy the Vampire Slayer.
I’ll keep repeating them until someone gets them:
Lord Kane
Papa Joe
Hmmm, all I can think of is Kane/Cain from the Command and Conquer series of games and I’m not even sure of the spelling (without cheating and Googling.)
That’s the one I was thinking of.
Ogden Wernstrom - Futurama
Terry Benedict
O’Brien
Big Daddy - would this be from “Cat on a Hot Tin Roof”? Although I never thought of him as a ‘villain’. Jerk, definitely, but villain?
Magua
Queeg
Kitchener
Magua is from “Last of the Mohicans.”
Queeg - The Caine Mutiny
Kitchener - Breaker Morant
Here’s a few probably obscure ones:
Eldrad
the Leviathans
Carlo Hesser
Nimue (or Nimuette)
Raven Darkholme
Fred J. Dukes
Bruno Antony
Terry Benedict - Oceans 11 & 12 (& 13, too)
The New and Improved Superman and muldoonthief are both correct.
No, it’s a different “Big Daddy.”
It’s not the British wrestler, either.
Queeg is also the backup computer that tried to eliminate Holly in an episode of Red Dwarf.
Queeg WAS Holly in disguise, playing a joke on the crew
A villain/ ess in the Doctor Who story The Hand Of Fear
Are the Leviathans the ones from Surface?
Carlo Hesser - One Life to Live.
Sorry, I can’t think of any to add.