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In the Negima and Nanoha crossover Equal and Opposite Attraction, Mind Rape seems to be on the menu. Its happened twice. Once with Arf when she was forced to watch Fate get tortured all over again. And again with Hayate, who again has to watch her knights get killed in front of her, but this time its BAD: Only Signum gets the quiet death she received in the series, since Vita gets impaled on an iron fence, Zafira gets beaten to death, and its implied that Shamal was raped on top of being killed. To top it off, Reinforce is revived, only to kill Nanoha and Fate right in front of Hayate, then proceeds to destroy the entire city, leaving Hayate the only living thing for miles. The chapter ends with one word:
In the Naruto/Negima crossover Happy Families Are All Alike, Evangeline tries to read Naruto's mind. The Kyuubi... hurts her. Literally tore her mind down to the foundations. Then Evangeline REBUILT HER MIND and pushed the demon out. It is implied that the Kyuubi does this with fair regularity to Naruto via nightmares.
My Little Castlevania: Just looking at Death's face causes whoever does so to relive every painful memory they have. The fact that Dirt Nap is unaffected by it is what clues Death and Actrise in to the fact that he might be an asset.
In The Return mind rape is Alexia's favourite recruitment tool. Convert someone into a succubus and mindrape them into submission.
In XSGCOM, this is standard procedure with every alien they don't consider "to valuable to cause brain damage". Yeah, X-Comareruthless
In Royal Heights, the Elite will occasionally undergo bizarre or downright terrifying shared dreams called Elite Visions created by the Headmaster of the school. These visions are meant to be of some assistance to the Elite in order for them to know about their future work on their new Utopia but it ultimately gives them a gander into pure nothingness, seeing themselves dissected and hooked up to a machine but still self aware. And the worst thing about that vision is that it's meant to truly happen to them at some point.
In Alexnandru Van Gordon's Teen Titans fanfic "Not Again", a telepathic OC ties Robin down and does this. He enters Robin's mind and forces both of them to experience the death of Robin's parents, as well as the other awful memories in Robin's head. The reason- to see if Robin is worthy to kidnap and adopt.
In Outside85's Teen Titans fanfic "Raven Rising, Book 2: Scars, Raven is captured in Tartarus (Greek hell) and subjected to torture involving getting constant visions of Amazons, Titans, and Justice Leaguers hurting and killing her. In this, it takes the trope literally when one of her visions is of Nightwing/Richard Grayson raping her. By the time a team of Amazons, Titans, and some Leaguers rescue her, Raven can no longer tell what is real and what is her torture.
In Forward, the "Inducer" type of psychics do this to people. The Academy has to keep them constantly sedated and under guard by combat drones or they'll drive the research staff insane, and this is mostly the ones who are too insane themselves to control how they influence minds. The ones who know what they're doing and understand how to influence people's minds can do far worse.
In the "Charity" story arc, this one almost becomes literal rape. An Inducer makes River and Jayne sexually attracted to one another to keep River distracted. They almost do the deed on a pile of crates right after surviving a fight with a small army of mercenaries, before Jayne realizes something is amiss. The chapter afterward involves River being directly mindraped repeatedly when she confronts the Inducer behind it all, and it ends with the Inducer taking control of her.
In the subsequent story arc, it gets worse. When River manages to briefly regain control of herself, she tries to fight back. The Inducer in question becomes pissed off and proceeds to brutally crush her mind by alternating between intense grief and guilt and intense pleasure and satisfaction.
In The Jaded Eyes Series dark!Harry/Tristan is fond of giving to his enemies all the pain he's ever experienced in his life or locking them in their worst nightmare. Also Tristan dumps three lifetimes worth of memories into Canon!Harry's head. These memories include being a mass murderer that's killed off almost all non-magical humans.
Dumbledore does this to Harry in Paraselenic. After Dumbledore realizes he's lost control of "his weapon," he traps Harry's mind in a Lotus-Eater Machine showing how everything could have been so perfect if he would only forfeit his pesky freewill and become a mindless slave for Dumbledore.
In Arabella's fanfic "The Very Secret Diary", all of the gruesome mind-rape that probably went on between Tom Riddle and Ginny Weasley in the second Harry Potter book is detailed to an uncomfortable degree. It's damn fine writing, though.
This Harry Potter fanfic is based around the idea that Ginny was repeatedly raped by Death eaters using Polyjuice potion to look like her father. It later all but mentions the trope by name, following Harry's reveal that Voldemort forced him to watch Ginny's literal rape and made him suicidal.
In The Elements of Harmony and the Savior of Worlds, during his original rampage Discord tortured Morning Glory's mind for days and days, leaving her almost completely unresponsive to those around her. And due to Rosedust isolating the Flutter Ponies in anger, Morning Glory spent thirteen hundred years like that.
CheckerMonarch from Getting Back on Your Hooves has done both this and the 'mundane' method facilitated by psychic methods. Using a dream infiltration spell (which is highly illegal for her to use at all) combined with Lucid Dreaming, she's a Dream Weaver capable of entering someone's dreams and manipulating them however she pleases.
Another Discord example: in Night Of The Shy, though no details have been given yet, it's revealed by Luna that he mind raped her and Celestia's parents so far past the Despair Event Horizon that they lost the will to live and violently refused to be fed, allowing themselves to waste away.
Nyx receives memory fragments from Nightmare Moon wherein she wants to kill Twilight Sparkle... the pony Nyx considers as her mother.
While the canon version of him's methods were (almost) too tame to count as this, the Pony POV Series version of Discord loves doing this. Everyone being Driven to Madness under his rule cases such psychological pain that pretty much everypony in Ponyville pretty much needs weeks of consoling and help to get back to some resemblance of their old selves (except Fluttershy, who's hackneyed job on Discord's part simply left her with a pathetic excuse for an Enemy Within who she browbeats easily). Applejack pretty much sums it up quite well:
Applejack: Ponyville used to be the nicest, simplest, all around friendly town ya could hope ta settle in. But now it's feelin' like a little filly whose lost her innocence a little bit too soon.
His psychic Mind Rape of Diamond Tiara persists weeks later and effectively manipulates her into freeing him from his prison again by threatening to harm her mother. Discord is still a statue at this point, it was all a lingering effect of his Mind Rape presumably as a back up plan.
The sexual angle is referenced when the Wonderbolts member Fleetfoot states that, because of what Discord did to her, she feels violated. Some readers even assumed it was ACTUAL rape until Word of God explained it. The worst part? Discord does every last bit of thisFor the Evulz.
Becoming a newfoal turns people into perpetuallysmiling, mindlessly cheeryzombies, with little (if any) free will of their own. How is very brutal - basically, the Newfoals' human souls are literally broken to pieces and then bound to Queen Celestia and Tirek's will. Even worse, according to the zebras' elder shaman Quagga, it is utterly impossible to repair said souls; only Mercy Killing them will make their souls whole again and set them free. Meaning even if the Queen and Tirek are defeated, only mass euthanasia will set their souls free.
The Last Train From Oblivion side-story shows the process from the perspective of the convert. Said convert is a female member of the PER and willingly lets herself be ponified. She then undergoes a "ponification matrix" that decides to design her new pony self into a perfect slave for the Solar Empire. She begs them to let her be a nurse (her old human occupation), but instead, she's "programmed" physically and mentally into becoming a Sex Slave for Royal Guards (despite her having problems with sex due to having been molested in her past). Be Careful What You Wish For, indeed.
It's also revealed that Queen Celestia placed a "geis" on the Royal Guards so that they serve her every command without question. Allof them. In fact, most of the natural born Equestrians have also been brainwashed to some extent; TCB!Apple Bloom describes it as feeling like her thoughts are slowly being replaced by an irrational hatred for humans and a desire to ponify every person she sees (though thankfully, she's able to break free from it).
And the corruption of the TCB!Mane Six, combined with an especially brutal form of And I Must Scream. They were all imprisoned in their own minds while dark personalities were implanted into their bodies to carry out the Queen's will. The girls basically possess the same amount of agency as a human being controlled by a Yeerk, and all they can do is helplessly watch as their bodies are used as tools to commit Moral Event Horizon grade acts on the humans. By the time Canon!Luna finds this out during a Journey to the Center of the Mind, the real TCB!Twilight is reduced to desperately begging and pleading with Luna to kill her, if only to end everyone else's suffering.
And even TCB!Celestia herself given what the Bag of Tirek did to her.
The Slender Man ficBy the Fire's Light feature Slender Man inflicting enough mental pain and anguish on his victims so that they forget everything else except for the pain and the Slender Man itself. This is done to strengthen the Slender Man since it runs on belief.
In Sonic X: Dark Chaos, the voice of Dark Tails either kills those who hear it outright or drives them violently insane. Cosmo nearly meets this fate in Episode 58, but her mother's amulet protects her from the worst effects. Venus, Alice and Trinity are not so lucky.
Reality Is Fluid: Eleya has a mental conversation with an Undine that proves extremely painful to her (represented by the Undine inflicting a Neck Lift and manual strangulation through most of the conversation). She came out with minor brain damage (nothing Star Trek medicine couldn't fix, though).
In Phasis, Shadow (the aggregate sentience of darkness fonons) fights by showing the characters illusions of their fears or desires. Some of them break out of it on their own, while others have to get help from someone else. In the end, Jade suffers the most lasting damage: just before the battle, he had realized what was going on and come up with a solution...then the battle made him forget not only what he'd figured out, but the memory of figuring it out in the first place.
The Things, written by Peter Watts and nominated for the Hugo Award (so you know it's well written), is The Thing (1982) from the alien's perspective. Though Childs' status is ambiguous in the movie, in the fanfic he has been taken over by the Thing, and just before his mind is consumed the following exchange takes place:
Thing (narrative): How little it knows. It knows even less than I do.
Childs: "I know enough, you motherfucker. You soul-stealing, shit-eating rapist."
The fancomic/fanfic, Taste of Revenge found here in comic form and fanfic form. (If you like the personification of the United States of America, Alfred F. Jones, please save yourself the guilt and disgust by not reading this. If you're not weak-stomached, go ahead and read this.) The basis of the story is that Alfred, or U.S.A. gets gang-raped by other countries for causing global recession, in the meantime getting seriously Mind-raped for all the shit he did in the past. It's a good read and worth your time, but the comic and the read is not Work Safe. The worst thing of it all, they think they're helping Alfred by teaching him a brutal lesson. Sure.... rape the world's last remaining superpower who has enough nukes to destroy you all. Real nice.
The AU Winter War had Aizen use both the Hogyoku andCold-Blooded Torture to Hollowfy and break high-level Shinigami to the point of generally unquestioning servitude, though final results depended on the individual (and were horrifying no matter what).
CheckerMonarch from Getting Back on Your Hooves, due to having Manipulation as her special talent, is quite adapt at doing the mundane version, but probably the most clear example is when she infiltrates Trixie's dreams and gives her a Breaking Lecture that leaves her so traumatized she is almost too terrified to actually go on stage for her public apology. Counts as mundane instead of psychic because she only used her words and nothing else.
For another example from pony-related Dark Fic, look no further than "Pattycakes". Part 1 has Fluttershy, saddled with a really creepy infantilism fetish, psychologically break Rainbow Dash and make her regress to a childlike state by forcing her to act like one until she totally gives up hope and internalises it. This takes...less than a day, and the most intense torture consists of forcing Dash to use a nappy and drink from a bottle, yet at the end Dash is completely convinced that her oldest friend is actually her mother and that she is let's go with twenty years younger than she actually is. Part 2 retconned it so that Fluttershy instead used a drug called "foalmula" to make Dash regress, and even lampshaded the rape angle to a degree by having Fluttershy comment that for Dash she'd abandoned her rule about only using foalmula for consensual age play. Things get creepier from there.
Unlike the canon version, the Pony POV Series version of Discord's breaking of the mane cast is treated as this, though for some of the group more than others and in part due to the psychic effects. However, what he does to Trixie most certainly counts, as like Twilight, he doesn't need to do the psychic version and effectively convinces her no one can even tell she exists by illusions and a nasty Breaking Speech. Even after he's been defeated, Trixie has been so psychologically broken she's still "Discorded" weeks later.
Pages Of Harmony takes this concept, runs with it, and exploits it in a variety of ways - Twilight uses Mind Rape on each of her friends to analyze their Elements in a quest for "preservation of harmony", altering their memories so completely that all of them go through permanent physical and psychological changes, most barely having any remnant of their old selves. Easily the most evident example is Rainbow Dash, who is reduced to being a self-cannibal in an attempt to rid herself of any loyalty to herself or others - a trait that becomes a self-destructive habit even after she dies. Her thoughts are then consumed with only one true desire: murder Twilight and make sure she burns in Tartarus. And this is just the first of the victims.
The Crack, aka Mind of a Hero, has Vlad use a device as an Emotion Bomb, which he claims will bring forth what Jung referred to as the shadow on Danny. To say that it didn't end well is putting it mildly. Both parties are still messed up about it seven years later to the point that Danny can't/won't have normal relationships.