The confrontation between Slade and Raven in "Birthmark" has the villain ripping her cloak, making her clothes magically disintegrate, and speeding up time to show her a vision of The End Of The World at her own hands. The experience is so traumatic it causes Raven to have a meltdown and release an enormous burst of magic energy that breaks the illusion but also renders her unconscious.
In "Haunted", Robin becomes convinced that Slade, who at this point is presumed dead, has returned. However, it is later revealed Robin is the only one who can actually see his nemesis, leading the other titans to conclude that their friend has gone insane. The episode ends with the revelation that Robin had been previously exposed to a hallucinogen while examining Slade's possessions, trapping him in an illusion in which he was doomed to fight an enemy he could never defeat.
What Raven did to Dr. Light during the opening teaser for "Nevermore" wasn't shown, but it is strongly implied that she used her demonic powers to damage his mind. After she loses control of her anger and drags him underneath her cloak with black tentacles, he comes out shivering, with his suit shattered and mumbling incoherently. In a later episode, Dr. Light is shown to be traumatized from this encounter, as he immediately surrenders and quietly agrees to go to jail when Raven confronts him.
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.
It happens to Galvatron again in the Season 3 episode 'Webworld' where he was taken to Torkulon by Cyclonus in order to cure his psychosis. All the therapies he went through fail leading to the therapists to use the Alya solution to lobotomise him. What happened next however was as soon as the planet invaded Galvatron's mind he entered its mind as well, learning its secret to destroying it while the planet was going haywire from his insanity.
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 episode "Only a Dream", Doctor Destiny (John Dee) uses his powers in a disturbing fashion - he traps his ex-wife 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. Then he goes after the League.
During the Thanagarian invasion, J'onn, in order to get some codes for a Thanagarian ship to retake the Watchtower, forces himself into Kragger's mind. The guy obviously resists, but J'onn overcomes him, suffering several physical manifestations of his psychic wounds in the process. 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.
Flash: I thought you said you couldn't read their minds.
J'onn (eyes glowing as he reaches for Lt. Kragger's head): I'll just have to try...harder.
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, 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 '90s 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.note 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".
The episode "Holly, Jolly Secrets" reveals that a man named Simon Petrikov found a cursed artifact that tormented him with visions of spirits and the impending apocalypse that would create the Land of Ooo. He fights it, but over time, he loses all his sanity, eventually becoming The Ice King.
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 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 through the link "Mgann...what have you done?
Arguably happens twice in Metalocalypse both times in the same episode. During the Revengencer's attack on Mordhaus, General Crozier shows up in an effort to protect Dethklok. Unfortunately, Selatcia chooses this precise moment to put his plan into action. He shows up out of thin air and subjects Crozier to a horrific series of visions which essentially leaves the General under his complete control. Then, just before he leaves, he locks eyes with a wounded Offdensen - an experience which quite literally kills the latter.
In the 2018 reboot of She-Ra and the Princesses of Power, Horde Prime inflicts this on Hordak, angered by Hordak's display of free will. He forcibly enters Hordak's mind and probes his most intimate memories (including Hordak's love for Entrapta and doubts about returning to the intergalactic Horde) as Hordak looks on in horror. When Prime mind-wipes Hordak, his expression goes blank and his eyes change from red to green.
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.
Near the end of The Amazing World of Gumball episode "The Castle", Nicole enters the house, which has been overtaken by local citizens, and orders all of the crashers to clean the mess they made. When Harold scoffs at her threat, Nicole gives him a Death Glare, where what he sees in her eyes are horrific apparitions, reducing him to tears as he takes a broom and sweeps the floor. Played for Laughs of course.
The trope is referenced by name in an episode of American Dad! where Stan is swindled by a car salesman... repeatedly.
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.
Rick and Morty: When Rick's ship is forbidden from using actual violence, it resorts to its idea of psychological warfare. In the case we witness, it involves finding out the captain of the squad currently aiming weapons at them had a son who drowned years ago, whipping up a clone of the captain's dead son to lower his guard, have the clone tell him to please step away from the ship, then melt before his eyes as the captain looks on, unable to stop his son from leaving him again. It's naturally horrendously effective, reducing the captain to a whimpering mess hugging the melted remains, and horrifying the rest of the squad enough for them to dump their weapons.
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..."
A very disturbing example happens in Season 2 of, Star Wars: The Clone Wars, and one being inflicted by the protagonists at that. Cad Bane stole a holocron containing a list of the Force Sensitive children for Palpatine. An interrogation by Obi-Wan and Windu yields no results, so cue Anakin:
Anakin:We'll have to use The Force to make him talk.
The end result of this (after Anakin reveals there simply is no other way) is the following:
Anakin: You will take us to the holocron.
Cad Bane: Jedi mind tricks don't work on me.
Anakin and Obi-Wan:You WILL take us to the holocron.
Cad Bane: Forget it!
Anakin, Obi-Wan and Windu: YOU WILL TAKE US TO THE HOLOCRON.
Cad Bane: I won't!
Anakin, Obi-Wan and Windu: AND YOU WILL TAKE US... NOW!!!
Cad Bane: I will take you... NO! GET OUT OF MY HEAD!!!
And then Anakin, being Anakin, suggests another attempt. The utterly TERRIFIED Bane finally caves in after that:
Anakin: Perhaps we should try... AGAIN.
Cad Bane (in a weak voice): I... will take you to the Holocron.
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.
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.
What Megatron in Transformers: Prime did to an amnesic Optimus/Orion 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.
This isn't even mentioning the Cortical Psychic Patch. Being a Decepticon technology, it's usually used to pry information out of captives.