The confrontation between Slade and Raven when Slade first returns includes Slade ripping her cloak, her clothes magically disintegrating, and her hair growing as he holds her immobilized, showing her a vision of The End Of The World at her own hands before tossing her unconscious from a roof. Many fans were quick to point out the similarities between what happens here (the attacker's attitude towards the victim while committing the assault and the effect it has on her) and an actual case of rape, which for a cartoon like this, was really saying a lot.
In addition, the entire episode 'Haunted' is just one gigantic Mind Rape.
What Raven did to Dr. Light during the opening teaser for "Nevermore" wasn't shown but strongly implied; she lost control of her anger and dragged him underneath her cloak with black tentacles and developed a demonic hiss and GlowingRed Eyes. He came out shivering with his suit shattered, mumbling incoherently. In a later episode, Dr. Light immediately surrenders and quietly agrees to go to jail when Raven confronts him. (She pretends to assume her demon form, and it terrifies him.) Ironically, her encounter with Slade occurs later in the same episode.
Poor Dr. Light. Mind Raped in two separate universes.
Tarantulas did this to Blackarachnia in Transformers: Beast Wars, hitching a ride inside her body, complete with a few creepy visuals of his head in triplicate and giant form hovering over her to show his domination of her mind. She went into his brain to retrieve information first, so if you've got a sick sense of humor you could say she was asking for it. She does, eventually, free herself from his control, and she recovers a bit more fully (and quickly) than most victims, but compare how seductive and flattering she acts towards him in the first season to how cold and distant she does in the second.
Also happened in Beast Machines to Silverbolt, by Megatron, via brainwashing him into becoming his sadistic vehicon general Jetstorm. When he recovered, his sappy, chivalrous persona was replaced with a brooding, rage-filled loner who bitterly dismissed his former idealistic self as "a fool [who] believed in things". If you doubt it, compare his description of being Jetstorm to Carrie's mom describing being raped physically by her husband.
Blackarachnia:"Nobody's judging you. You were under Megatron's control. Join us, and you can avenge yourself."
Silverbolt:"You still don't get it, do you? I don't hate Megatron for what he made me do. He freed me from my code of honor, and I revelled in it. Don't you see? I… enjoyed it. I don't know what I am anymore."
Megatron did this to amnesia!Starscream in Energon, to get Starscream back on the Decepticon side. It was also a fairly obvious metaphor for something... else.
What? You mean when Megatron traps Starscream in a darkened room, then repeatedly commands his struggling and protesting victim to "say his name" while simultaneously stabbing him with his massive sword? What could possibly be suspect about that?
And looking back to 1986, this is what Unicron has to do to Galvatron to enforce his loyalty, because Galvatron is Megatron wearing a new body and name, and Megatron is mentally incapable of being second banana.
And then in the season before the movie we get "The Secret of Omega Supreme," where a flashback shows Devastator (composed of Omega's former friends) holding him down while Megatron's robo-smasher device attempts to re-program Omega into a Decepticon. One wonders how much of Omega's personality shift was due to the partial reprogramming and how much was due to just the overall experience.
Devastator: "Quit squirming! This is for your own good! HAHAHAHHAHAHAH!"
In the second season, Doctor Destiny (John Dee) uses his powers in a disturbing fashion - he traps his ex-girlfriend in a nightmare. In one creepy scene, he removes his clothes in front of her, before "putting on" his costume. She ends up becoming the first person in the series to actually die by action of a supervillain.
During the Thanagarian invasion, Martian Manhunter, in order to get some codes for a Thanagarian ship to retake the Watchtower, forces himself into a Thanagarian's mind. The guy obviously resists, but MM overcomes him. He's left mostly a vegetable, and the next time we see him, he's hooked up into a mech and can barely string sentences together. Thinking about a hero mind raping someone just to learn to fly a ship is what terrors are made of.
Flash: I thought you said you couldn't read their minds.
Martian Manhunter (eyes glowing as he reaches for Lt. Kragger's head): I'll just have to try...harder. The Thanagarian also has one of those looks on his face.
And then there's Ace of the Royal Flush Gang, who can make people insane simply by staring at them. The Joker takes her out of the government containment facility where she was held, and attempts to use her powers to drive the entire planet insane with a reality show. According to Joker, his insanity protects him from her milder mind-rapes, but when Ace realizes that he's no better than the government agents who kidnapped her, she makes him so insane that he goes into a coma (those who think of Batman Beyond as an alternate timeline like to believe that Joker remained in this state for the rest of his life), and the only reason he might have recovered is because he's too crazy to be properly Mind Raped.
In the episode A Knight of ShadowsMartian Manhunter is also mind raped by Morgan Le Fay in hopes that if she can convince him to fork over the philosophers stone for the illusion of his dead family. He's fine after the episode but for the duration of it he's quite screwed up by it.
X-Men: You wouldn't expect this from him considering his Mind Over Manners approach, but Xavier applied some harsh enlightenment to Magneto about his violent ways by having him relive his memories of the Holocaust (or the generic war he lived through; it was a children's cartoon so they couldn't use the H-word). It may have had a point in teaching him that violence is wrong, as he spent the rest of the series reforming from his villainous ways but it is still forcing someone to relive his darkest memories.
In the "Proteus" two-parter, the eponymous Psychopathic Manchild with reality-warping powers "physics-raped" Wolverine: He wills him to get torn in half, first horizontally, then vertically, and then melts him into a puddle of green slime, while his claws turn into writhing adamantium asps and try to bite him. When Proteus flies off, Logan "oozes" back into shape, sobbing into his hands from the experience. Afterward, even Wolverine, the archetype of the Nineties Anti-Hero, was horrified still many episodes later.
In "A Rogue's Tale", Rogue's mind is invaded by the memory/personality of Ms. Marvel, a leftover from having absorbed her powers for good, and she is tormented by the guilt and shame of it until Jean locks that part of her away.
Then there's what Dark Phoenix did to Mastermind after realizing he was trying to control her.
In one episode of The Powerpuff Girls, the girls face the Sandman, who wants to put everyone in the world to sleep so that he can be free from his duty of putting people across the world to sleep and get some rest for himself. The girls decide that to beat him (after being put to sleep themselves and finding that they can enter dreams) is to give him a nightmare so bad that he will never want to sleep again. What follows can only be described as Mind Rape.
In Adventures Of The Galaxy Rangers, the Psychocrypt is shown to be a particularly nasty version. It's an extremely painful process that rips the person's soul out of them, shoves it in a Soul Jar, and then turns the Life Energy into a vessel through which the Queen could see and hear. Even your most intimate thoughts were hers.
She also created a "dream making" device, powered by Eliza's crystal, to rather casually rape Zachary (and Eliza) on a nightly basis for a while. Zach, who is normally The Stoic, was shown a couple times collapsing and screaming from the sheer pain of it.
There was also the Poe Mutant Sensation Doll from "One Million Emotions." It's an Artifact of Doom that was designed as a work of fine art by the culture who created it. Anyone else? Touch it, and it's "the emotional electric chair." One of the Rogues Gallery forced one of his Mooks to touch the thing. Said mook screams from the overload, and is later seen to be a gibbering wreck. Another of the Rogues Gallery is later reduced to blubbering for his mommy after making the mistake of grabbing it.*
They're both okay in later episodes, though.
This was also one of the many nasty tricks the Scarecrow was capable of.
We also had the Mindnet, a means of artificial telepathy (or enhancement of what was already there) used in "Mindnet" and "Battle of the Bandits".
Adventure Time reveals during the episode "Holly, Jolly Secrets" that a man named Simon Petrikov was mind raped over the course of several hundred years, by a cursed artifact. He fights it, but over time, he loses all his sanity, eventually becoming The Ice King.
Played for laughs on Phineas and Ferb. When the super computer the kids built scans the entire Tri-State Area, Norm the robot covers his ears and says, "Get out of my mind!"
In Young Justice, Psimon did this to M'gann by invading her mind and torturing her with the threat of revealing her darkest secret: that she isn't a Green-Skinned Space Babe, but an inhuman-looking White Martian. M'gann then returns the favor, unleashing her full psychic power to turn Psimon into a drooling vegetable. In season 2, M'gann violently rips out information from the minds of two aliens whose brains can't be read through less invasive psychic methods, leaving them drooling and unresponsive.
Then we discover that the reason Super-Boy broke up with her was because when he confronted her with her actions, she tried to mind rape him so he'd forget that he was ever angry with her.Yeah.
And things go downhill later on when, after meeting up with Reverse Mole Aqualad for supposedly killing Artemis, she delivers a Mind Rape so bad that he's left unresponsive and she learned too late that Aqualad was Good All Along while Artemis—still alive and calling herself Tigress—asks her trough the link "Mgann...what have you done?
The Shaman in Sym-Bionic Titan does this to both Lance and Ilana. Lance with memories of his childhood and his Disappeared Dad, Ilana with her fear of Galaluna's fate, believing that she has "abandoned" her people.
In one episode of Transformers, a Quintesson placed a Junkion in a bare cell to see how long it would take someone accustomed to the most cluttered environment in the galaxy to break down when deprived of stimulation. Almost immediately, the Junkion starts tearing at the walls and ripping up the floor. Disappointed at how quickly his subject collapsed, the scientist turns off the monitor. Later, the trope is subverted when the scientist checks back to see if anything has changed, and sees the Junkion, perfectly relaxed, laying back on an improvised couch. The Junkion hadn't suffered a breakdown; he'd just been redecorating.
Season 3 also had theSon show Anakin a vision of his future as he kills his wife, turns against the Jedi, and blows up the planet of Alderaan. He's so horrified that it breaks him, making him completely obedient to the Son.
Played for laughs in the SpongeBob SquarePants episode 'Big Pink Loser', Patrick decides that the easiest way to win an award for something is to copy everything that Spongebob does. At one point Spongebob began behaving very randomly, but Patrick was able to copy him. Cue Spongebob thinking "At least I'm safe inside my mind." and a horrified look on Spongebob's face when we hear Patrick's thoughts, apparently pushed into Spongebob's mind... "At least I'm safe inside my mind..."
The trope is referenced by name in an episode of American Dad where Stan is swindled by a car salesman... repeatedly.
What Megatron in Transformers Prime did to an amnesic Optimus/Opion could be considered this, given the way Megatron took advantage of the latter. Later after Optimus regained his memories but doesn't remember his time spent with Megatron, Megatron uses this to taunt him. The look on Optimus's face as he realized what he had done is uncomfortable to watch.
Horrifically done to Korra in The Legend of Korra by Amon. Just as she was starting to gain her confidence about facing him back, he ambushes her and has her completely at his mercy. He tells her that he can't do anything to her yet as it would only make her a martyr but makes it clear that she will see everything destroyed and that she will be his last target. Even worse, is that it's treated like a real rape. Korra suffers a complete breakdown afterwards.
Amon stripping Tahno of his bending also qualifies. Especially with the way the scene is shot, the way Amon touches him, and his reaction the next episode.