Hero on villain example: In The Crow, Eric Draven can experience the sensations and memories of others through touch. When he picks up from Officer Albrecht what his fiancee Shelly went through before she died (thirty hours of surgery and intensive care), he's staggered by it all — though he recovers, as he's already undead and probably quite insane from a certain point of view. He also demonstrates another ability — to transfer the things he knows through touch, which he uses to full retributive effect on the final target of his Roaring Rampage of Revenge, Big Bad Top Dollar, whose orders were responsible for Shelly getting raped and beaten to death, and Eric himself being gunned down. Top Dollar, who while evil is quite alive and mostly sane, proves to be unable to stand "thirty hours of pain," all in one shot...
In Star Trek VI, of all places, Spock's mind-meld with Valeris definitely comes close to this trope, and it's really uncomfortable to watch. The only saving grace being that it is made obvious Spock is almost equally affected by his actions; self inflicted Mind Rape, anyone?
The Novelization, recognizing the implications of Spock's act, first explicitly declares a forced mind meld to fall into this category and then explains that Spock didn't force her, he mentally convinced her of the seriousness of the situation and she gave in willingly. Which, uh, doesn't explain the screaming at the end.
In Star Trek: Nemesis (2002), Deanna Troi is literally mind raped by the villain who invades her mind when she and Riker are about to do the business. That wasn't the first time this happened to poor Troi. One episode of TNG features an alien passenger aboard the Enterprise mind raping the crew in the figurative sense, but he mindrapes Troi in the literal sense, and fairly graphically. The act is even flat out referred to as "a form of rape" at one point, in case anyone didn't quite get the implications..
Of the Brown Note variety in Star Trek: Into Darkness. When Spock is fighting Khan, he briefly mind melds with him. Whether Spock just transferred his feelings of grief and rage or did something else, Khan lets go of him and stumbles around a bit before regaining his feet. It's also possible that, given Khan was attempting to physically crush his skull at the time, Spock was sharing the physical pain he was experiencing at the time.
Samara Morgan from The Ring has a history of Mind Rape, though not always intentional. Her biological mother tried to drown her shortly after giving birth because she claims Samara "told her to". She caused her adoptive mother terrifying visions for years and was forced to live in a barn, where the horses got a taste of it and ran themselves off a cliff to get away. Fast forward to her killing years, where she apparently Mind Rapes her victims enough to literally scare them to death. Any witnesses get enough second-hand Mind Rape to end up as blank-staring mental patients. Lastly, the scene from The Ring Two, where Samara (possessing Aiden) mind-rapes (or perhaps mind-tricks) a doctor into suicide. Oh, and her video's pretty fucked up, too.
Event Horizon was full of mind rape of the rescue crew by the hellish entities that came from another dimension - which is worse than what most of you would imagine as "Hell" - via their deepest guilt, and causing several members of the crew to go insane, with one of them ripping out his eyes, mutilating himself and vivisecting a crewmate. Another one of the crewmembers who accidentally fell into the portal and was pulled back out after a moment went temporarily insane and tried to throw himself out of an airlock, telling the rest of the crew that "if you had seen what I've seen, you wouldn't try to stop me."
In The Lawnmower Man, there are two instances of mind rape by the protagonist/villain, Jobe. One is when he takes his girlfriend Marie into cyberspace and they try to make love; he loses control of his powers and ends up accidentally mind-raping her instead, leaving her catatonic. The second time is when Jobe, who's now both more in control of his growing powers and becoming more villainous, psychically unleashes a "Lawnmower Man" inside the head of a bully, purposely rendering him catatonic as well.
In Push, Cassie lures her Evil Counterpart, the Triad Watcher, into getting sneak attacked by a Wiper, who wipes out her entire memory of her family and knocks her unconscious. And Cassie is supposed to be one of the heroes.
Really any of the "Pushers" in this movie could qualify, consider how many peoples' memories they rewrite or how the actions they force people to do directly. Kira, to escape a team of Division agents pushes one to think he has a brother that the other killed. The agent sees his partner brutally murder his "brother" and shoots his partner dead. Even after he realized he was pushed, he still remembered growing up together with his brother and still felt the grief and shock of his death.
In The Avengers, Loki uses his staff to mind control Hawkeye, Erik Selvig, and a few other S.H.I.E.L.D. agents. Later, when Hawkeye discusses the experience, his description has heavy shades of this.
The thing is, it's all a setup on her part. She probably didn't know exactly what he was going to say, but she went into it intending to play it that way.
In a deleted scene from Dogma, Azrael subjects Bethany to a vision of what Hell is like thanks to mankind's need to be punished. The script describes it as "ten seconds... of the most fucked up and disturbing imagery that can be crammed into 240 frames of film." Afterward, Bethany convulses uncontrollably from the mental trauma.
The title character in Tamara does this to nearly everyone she touches, but special mention goes out to what she does to Roger, forcing him to experience what it's like being Buried Alive (in graphic detail), and to Keisha, exploiting her insecurity over her body by making her imagine that she's literally vomiting her guts out.
Taken to its most literal extreme in Dredd with Judge Anderson, who's psychic, and Kay. Since her abilities are always on, he tries to get to her by imagining himself actually raping her. She smacks him with her gun to make him knock it off. Later, during their Battle in the Center of the Mind, he tries it again. This time, however, Anderson is ready and changes the experience somewhat. Not only does he reveal what she wants to know, when it's all over he's pissed himself.
In the Stargate SG-1 movie The Ark of Truth, Daniel, Vala, and Tomin are tortured by the Priors of the Ori. The Ori appear to be chanting and using their psychic powers to reduce the good guys to weeping messes.
In End of Days, Satan screws with Jericho by forcing him to relive the murder of his wife and child in a home invasion he wasn't there to stop.
The plot of A Clockwork Orange is nicely summed up by this trope; the villain protagonist is tortured mentally to the point where his ultra-violent hobbies cause him pain, to achieve a form of brainwashing that will "reform" him.