Edward Nygma / The Riddler (Gotham)
With an eidetic memory, it's impossible to outwit someone like Edward Nygma, also known as The Riddler. And, if you add the knowledge to explosives and his split personality disorder, you'll have a genius criminal at hand. Edward was a former forensic scientist working for the Gotham City Police Department with a penchant for speaking in riddles. He later went down a path of criminal activity after murdering Tom Dougherty to protect Kristen Kringle and later killed Kringle by accident as well. These incidents woke his other criminal persona. Hence, the Riddler.
Lex Luthor (Smallville)
Superman became Superman not only because of his powers but because his arch nemesis was no other than a human named Lex Luthor. That’s right. A human—but with an intellect unlike no other. Notoriously brilliant, actually. He could create weapons that could kill the Man of Steel himself and proved to be the biggest villains in the history of Superman’s life. He even created multiple clones of himself for the sake of his own survival. Sadly, he resorted to murder when he finally decided to stab his sister to her death.
Michael Scofield (Prison Break)
Who would orchestrate a bank robbery to be imprisoned? Michael Scofield would! After he graduated as a Magna Cum Laude in Civil Engineering, Michael threw that away to save his brother Lincoln after the latter was sentenced to death. With a strategic mind like Michael’s, he created an elaborate plan to break his older brother out from incarceration.
Gabriel Gray / Sylar (Heroes)
This is a prime example of not everyone deserving to get what's coming to them. Sylar is what one might consider a genius beyond intellect. His ability to understand things and acquire them was nothing short of amazing, but his process in doing so made him a killer. For him to be able to understand and acquire other people’s abilities, he would have to cut open someone’s head to see how their brains function.
Eli Pope / Rowan (Scandal)
In the universe of Scandal, whoever runs the covert government agency known as B613 also runs the country covertly. Eli Pope, also known as Rowan, used to be one of its commanding officers. Meaning, he got to play around as god while choosing who gets to live and who gets to die. Because of that, his prodigal daughter Olivia Pope had him kept under her wings.