Technically, this happens with EVERY Angel other than Tabris (also known as Kaworu) even in the original series. Think about it, the AT field is supposed to be your barrier that isolates your true self (ie your soul) from others. Angels and Evas are somehow able to project this (leading to an idea that Angels are actually the most isolated, most terrified and most alone creatures in any anime). So when an Eva rips apart an Angel's field it is basically RAPING the Angel's soul. Not quite Mind Rape, but Soul Rape is as close as it gets.
Not to mention they do this passively. Being exposed to an angel's AT field typically results in your very sense of individuality being gradually overwhelmed. Not likely to be pleasant at all, even besides the fact that this is likely to dissolve you into Tang.
Paprika gets pinned to a table like a butterfly and then painfully has her skin removed, revealing a naked Dr. Chiba underneath. Made creepier by Osanai's dialogue. Also occurs among people who watch the movie as well.
Mai's descent into darkness began with the Dark Game between Malik and Mai, where Malik erases people from her memory, uses bondage-looking cards (for extra symbolism), and causes her to visualize herself trapped in an hourglass as she slowly dies. Yugi ultimately saves her, but Mai is traumatized afterward - plagued by nightmares, unable to enjoy dueling, even when she wins, and helplessly lonely. In desperation to escape the pain, she joins the cult, Doma.
Less rape-like versions of this are the point of the "Penalty Games" dealt to losers of Dark Games, especially the ones used in the manga and series 0 of the anime by the Pharaoh himself. Possibly the most important of these is the "Experience of Death" used against Kaiba, which inspires the creation of the holographic duel system used in the remainder of the series. The second anime lightens the Pharaoh's image somewhat by just replacing all instances of this with "Mind Crush", which does vaguely shown mental damage to the target.
This also happens in the final arc of GX: the final villain, Darkness, traps people in nightmares where all their hopes are dashed repeatedly until they give in to despair and all outside proof of their existences are erased.
Before this, poor Jaden gets in on the act! The Hero is trapped within his own soul, constantly told that because of him all of his friends have died and that all he has is himself. And it's very sad if you think about it. The one doing the raping is the Supreme King AKA: Jaden's Super-Powered Evil Side.
In Yu Gi Oh Zexal Tron does this to Droite, forcibly stealing her memories of Kaito (whom she's secretly in love with) and leaving her psychologically scarred, sobbing in Yuma's arms. To make this worse, he laughs at her like a sadist after doing it.
The three sub-villains of Sailor Moon Super S examined the dreams of pure-hearted people (one attacks young girls, another attacks older women, and the last one goes against males of all ages) to determine if Pegasus was hiding there... by forcibly sticking their head into the victim's "dream mirror". While the victim screams in pain or discomfort. Usually after seducing the poor Jane/John Doe to draw him/her to a secluded spot. The symbolism was very... subtle.
In the R season, Mamoru abandons Usagi because he's been having really disturbing dreams where she dies. He later finds out that these dreams were sent by someone else, wanting to test his bond with Usagi.The weird thing? Who sent them was... his own future self, King Endymion. Yes, Mamoru has been mind-raping himself, in a sense.
Wiseman tries to do this to Usagi in R, trying to convince her that Chibi-Usa and Mamoru don't care about her and have forgotten about her, including showing her fake memories he made himself. Her faith in them wavers for a moment but she ultimately snaps out of it.
Digimon Tamers features a digital Eldritch Abomination that uses human despair to create weapons. One of the secondary characters, who also happens to be a sweet and kind little girl with hidden Mommy issueswho has just seen her Digimon partner die, is subjected to several weeks of having her most horrible memories played over and over (specially those related to there), as if she were there and with full emotional intensity, so her angst can power up aforementioned Eldritch Abomination. Break the Cutie taken to levels even Eva would envy.
Also, the J-Reaper (Agent D-Reaper 01) actually manages to partially mind rape Takato, or the main character, with her "mind scan" attack (really obvious name), just before revealing herself in Episode 45 (in the park), quote "I don't feel well" unquote. Who would?!
Which shows how it mind rapes! First, it collects information on the target. Then, it confuses the target and/or recalls past memories/experiences, lowering the target's defence's which allow it to synchronize thought processes, thus gaining access to the target's mind. Finally, it suggests new thoughts into the target, completing the manipulation. Note that this is very similar to real world hypnotic suggestion. Takato was only one step away, because his partner digimon managed to prevent the full process.
Digimon Savers: MetalPhantomon does this to the heroes, forcing them to either experience nightmares or to relive their worst life experiences in order to consume their hearts.
Oh, God, Zeta Gundam... Several series have aired since that one, and Gundam has yet to show a protagonist who's gotten worked over as badly as Kamille Bidan did by Paptimus Scirocco.
ZZ Gundam had an instance of a hero performing it: when Haman Karn shoots a girl named Leina, her older brother and The Hero Judau gets so utterly pissed off that he enters Tranquil Fury mode and his Newtype powers manifest a demonic aura that so utterly terrifies Haman that she runs to her room sobbing. This is the woman who called Char "weak" and shrugged off both Kamille's and Scirocco's mental assaults with relative ease. Every Newtype for miles around felt Judau's rage at that point.
Victory Gundam comes close, with the Angel Halo installation. It basically uses twenty-thousand Newtype "psychikers" to amplify the powers of a single Newtype who can then use it to Mind Rapethe whole of the Earth Sphere if she so desires. Zanscare planned on using it on Earth to regress people to an infantile state of mind so they'd all die off and leave the Earth "purified". Fortunately for everyone involved, they had the bad judgement to place Shakti in control of it. Earlier, when testing its effects, they tried to use it to cause Uso to lose his will to fight, first by bombarding him with images of peace and happiness, then with scenes of terror and pain.
Gundam Seed: A more minor case, some would say Rau Le Crueset's final words had this effect on Kira Yamato, as in the sequel we first see Kira as mostly quiet man, always deep in his thoughts, staring outwards at the world, possibly depressed.
Kira's mental state at the beginning of Destiny is based on real-life veterans of war. After seeing so much horror, pain, and death... it does a number on one's psyche, even if you manage to live through it.
Gundam 00: Awakening of the Trailblazer has the ELS accidentally mindraping Setsuna when he tries to tap into their Hive Mind using Trans-Am Burst and tell them to back off. The sheer amount of alien data overwhelms him so utterly Setsuna suffers brain damage and lies in a coma for weeks. Even though as an Innovator, Setsuna is supposed to be superior to normal humans! Then he comes back for a second dose at the end of the film but endures this time because he dumped the excess data through Tieria into Veda. And that's not counting what he might've experienced on the ELS home planet for several decades.
The 9th episode of Gundam Evolve shows the protagonist, Yurii Ajissah the Red Snake, getting mind raped by the Geminus, an ultimate Psycho Weapon that has decimated the Earth Federal fleet, before being rescued by the White Unicorn, who appears to be Amuro Ray.
In Saint Seiya, ex-Dragon and actual Aloof Big Brother Phoenix Ikki often uses an attack called "Phoenix Genma Ken", which destroys his opponent's mind by trapping them in horrifying visions embodying their deepest, hidden fears, which are indistinguishable from reality. Afterwards, most opponents are left as empty, catatonic shells, their spirits dead. However, Ikki himself gets an absolutely brutal taste of his own medicine as he fights VirgoShaka during the Sanctuary saga: he is shown images of the Seven Stages of Hell, then is given horrifying visions of him and his brother as kids in the Netherworld, and then is progressively stripped of his five physical senses. Painfully..
Virgo ShakaMind Rapes pretty much everybody, including the viewers who are left struggling with slight Viewer Gender Confusion, mindrapes his own religion (since when did Buddhists kill in the name of Athena?) and finally mindrapes Saga, Shura and Camus with a very cruel Thanatos Gambit resulting in his own (perfectly planned) death-and their own overwhelming guilt and the loss of their senses.Charming. Plus he makes everyone cry Manly Tears, although in Saint Seiya that's not unusual.
In one of the non-canon old movies, Warriors of the Holy Battle, Fallen Angel Throne Moa also was pretty good at this, manipulating his enemies's memories to weaken them and then give 'em the last hit...
Harry's attempts to "hack" Melfina in Outlaw Star. They weren't successful on his part, but the imagery was definitely there (especially so when considering that Gene was tipped off to the first one by Harry's rather...excited reaction). Melfina figured out how to Stop Him, though.
What Mao does to Shirley Fenette. She was very mentally unstable after learning the truth about her crush, Lelouch, and his role in her father's death and shooting a knight of honor like Viletta. Soon, Mao made it worse by using his Psychic Powers to read her frail mind and cruelly play with her to reinforce her idea of shooting Lelouch. It was so bad that Lelouch had to mind rape her again to try fixing the damage, using his Geass to give her Laser-Guided Amnesia.
Actually what Mao did to Shirley was more Mind Probe, considering what had just happened to her: she was already broken from her and others's actions. To see him deliver a full force mind rape, look at what he does to Suzaku a few episodes later...
What C.C. does to Suzaku to stop him from attacking Lelouch would also qualify; she shows him memories of his dead father, ex-Prime Minister Genbu Kururugi, who Suzaku himself killed as a young boy. It's so bad that Suzaku falls into a catatonic state and is traumatised for a while afterward. Partially excusable in that C.C. admits she had absolutely no idea what she made Suzaku see; they even mention at the end of the episode that they had to wait until the Lancelot ran out of power to pull a trembling Suzaku out of the cockpit because he freaked out and started shooting everything. Several episodes later, as mentioned above, Mao also brings the issue up, manipulating Suzaku in a similar way he did Shirley, by reading his mind and mocking what he did to his father as well as his guilt over it.
It gets even better: when Lelouch tries to convince C.C. to escape before Suzaku pulls himself together, he grabs her shoulder and breaks her concentration, causing C.C. to accidentally Mind Rape herself. And Lelouch to witness both.
Later, C.C. does it to Suzaku a second time, as well as hitting a couple of random bodyguards with the same power; in this case it's completely accidental, as a side-effect of Lelouch's Geass becoming permanent apparently boosts her own powers.
According to one of the licensed side-novels for the show, an adolescent Mao used his power to manipulate an entire village in China into destroying itself by exposing the skeletons in everyone's closets. So, if anything, he's a practiced hand at the Mind Rape.
And the second season reveals that during the Time Skip, the Emperor used his own Geass to give Lelouch Fake Memories. Not a traditional Mind Rape, but the scene gets almost uncomfortably close to an actual rape, with Suzaku holding Lelouch down and Lelouch begging for him to stop.
To make things worse, Charles also mind-raped Nunnally to make her believe her mother Marianne had been murdered in front of her, mixing this with having the seven-year-old girl crippled to make the whole deal more believable. As a result, poor Nunnally was not only confined to a wheelchair, but also went blind out of trauma. His wife Marianne constantly erased and rewrote the memories of Anya Earlstreim, an Action Girl who had become her vessel through Grand Theft Me, to cover all of this up. The poor girl was left as anemotionless wreck, as she never really knew which memories were truly hers and which were not..
If Lelouch uses his Geass to order someone with strong enough willpower to do something utterly abhorrent to them, a Mind Rape-like effect will ensue when the will of the victim tries to fight off the Geass. It happened twice in the series... and aptly enough, both of them were his sisters. He causes mind rapes many more times than that by forcing people to do things against their will often leaving them an emotional wreck afterward.
The Sol Eleven Master Pei La Cain does this a couple of times to Guy in GaoGaiGar FINAL, showing disjointed flashes of various scenes from both the original anime and the OVA.
In a bizarre example of a good guy doing this, Kurama in YuYu Hakusho executes an eternal punishment on the Elder Toguro by trapping him in his own subconscious with a treacherous plant.
Last ExileDio's Rite of Covenant is basically a case of Mind Rape that turns him into a semi-catatonic killing machine.
In Chrono Crusade, Pandemonium does this pretty much constantly, mentally assaulting anyone and anything she comes in contact with. In fact, Joshua's insanity wasn't caused by a total power overload like originally assumed, but by the fact that Chrono's horns mentally linked Joshua to Pandemonium, meaning he was mind-raped almost every waking moment of his life.
In Get Backers, a surprising good-guy (well, relativelygood) example: Ban Midou has the power to show people a perfect illusion for one minute, and he often uses this ability to Mind Rape his enemies. And even when he actually doesn't use it on people (and simply fools them into thinking he used it), it still ends up mindraping them when they try to wrap their mind around when exactly he actually did use it.
In InuYasha, about one third of the way through the plot, Naraku traps the gang in a field of mist and some sort of root-like plant which traps them and forces them to see hallucinations of which they each fear the most: Miroku's hallucination is his Wind Tunnel breaking its constraints and swallowing him slowly from the hand up; Sango hallucinates about Kohaku killing everybody; Shippo hallucinates that he's completely alone and everyone else in the group has disappeared (leaving only their clothes behind); and Inuyasha hallucinates about Kikyo and him dying together. He's the only one to snap out of it on his own, because he (unsurprisingly) remembers that he needs to protect Kagome.
Virtually any character trapped by a Mangekyo Sharingan user's Tsukuyomi on Naruto is forced to endure horrific torture, both mental and physical (the pain is entirely real, although the torture doesn't leave marks on the victim's body), for what appears to the subject as any amount of time that the user deems fit, effectively leaving the victim crippled and in a state of mental collapse.
Various genjutsu can border on this too, as they can conjure up and play on the victim's worst fears and insecurities.
Sasuke was under this at age 7 and suddenly witnessed the death of his entire clan, including his mother and father, as murdered by his older brother.
Special mention goes to Manga Chapters 257-260 where Yuura, being used as a puppet by Itachi, does this to Naruto, trapping him in an illusion where he thinks Sasuke is trying to strangle him, and Kakashi, Gaara, and Sakura are expressing how disappointed and angry they are with him while appearing on different parts of his body. It's enough to bring Naruto to tears. Thankfully, Sakura and Chiyo manage to dispel the Genjutsu with their chakra.
And in 497 Kyuubi musters up all of the residual loneliness, anger, and hatred buried in Naruto's subconscious and unleashes it on Naruto in order an attempt to win a mental battle. And he wins it. With his own will and the help of a chakra-ghost of his mom..
In chapter 583 Kabuto's adoptive mother is brainwashed to see Kabuto as a stranger to kill and another boy as Kabuto. Quite the Tear Jerker.
Road does this to Lavi in D.Gray-Man when she enters his mind to manipulate his conflicted feelings about becoming the next Bookman and his affection for his friends.
In the anime she also mind rapes General Kevin Yeegar, tormenting him with his failure to prevent the death of his class by an akuma-possessed child. (He was a schoolteacher before becoming an exorcist.) This leads to his Heroic BSOD, leaving him helpless against Tyki Mikk's finishing blow.
Hitomi Kanzaki, in Vision of Escaflowne, gets mind-raped almost every time she has a vision or does a tarot card reading. In Episode 11 it's so bad that the poor girl almost dies because her heart stops out of the sheer force of said mind rape (to be fair, she did see Dilandau bloodily kill a shapeshifter by crushing him to death with his Guymelef's bare hands). Also forces Hitomi to declare (to Van, Allen, and almost every other main character) that she hates their world and wants to be sent back home.
Dr. Muraki from Descendants of Darkness does this numerous times to most of the people he meets (showing Hisoka memories of him raping him, reminding Tsuzuki that he's not human, guilt-tripping Tsubaki-hime and making her think she killed her friend, etc.)
Often happens in Dot Hack. The very act of a human being Data Drained is...not healthy; but Tsukasa and Sora in .hack//SIGN really get their minds slammed by Morganna. Tsukasa's was particularly gruesome in "Tempest", forced to lie down, floated into the sky, and her power stomps on his mind and rips his clothes. He spends the next episodes catatonic, but manages to claw his way back to sanity. Sora's was so bad (in episode "Return") that after he was finally freed his mind completely blanked out the experience. So much that he didn't realize when he played the game again as Haseo. AIDA in Dot Hack GU also gives its special whammy to its victims.
The series Gokudo has an episode in which gods try to crush the minds of Gokudo and Rubet to take their bodies, by convincing them that their life is painful and worthless. Of course the gods lose and get enslaved by these humans instead. It seem to be useless to even try to do mind attacks on anti-heroes.
In Berserk, Ubik, one of the God Hand, pulls an epic one on Griffith to get him to carry out the sacrifices to become a demon god. It works.
Higurashi no Naku Koro ni; most of the main cast are batshit insane, and poor Keiichi gets mind raped pretty much every arc. The victims of Hinamizawa Syndrome are seeing horrifying hallucinations of their friends acting like demonic entities or something similar disturbing to make them Ax-Crazy Psychos. Hinamizawa Syndrome is a mind raping disease.
Keiichi? Try Rika, who has lived through hundreds and hundreds of years of mind rape and can't do a damn thing about it, other than restart and live through the torturous process all over again.
Rave Master's Sieg Hart uses this on Haru, trapping him in a barrier that turns every single thought he makes into visions where his loved ones gruesomely kill themselves for him.
Anime only, in the "New Captain Sh?suke Amagai arc" where Hanza Nukui uses his Bakk?t?, Saiga, to look into Ichigo's memories, and then tortures him with the memories of the death of his mother. Hanza makes it so she tries to choke Ichigo, making it so Ichigo can't harm her or fight back. He tells Ichigo he'll only be able to save himself if he can kill his mother. However, before Ichigo chokes to death, the pleasant memories with his mother comes up from deep within him. Ichigo then tells his mother how much everybody misses her. Before she vanishes, she smiles after Ichigo thanks her for protecting him that day.
Don't forget Aizen's expy and Big Bad in the X-Cution arc Shukuro Tsukishima. Who can use the psychic variant by manipulating the memories of the person who will be useful to his plans and make them believe he's always been thereand combine it with the second by forcing Ichigo to interact with him in the surroundings of his brainwashed loved ones, doing it so well that when Ichigo cracks and attacks him, everyone thinks Ichigo's the one in the wrong and is going mad. So Ichigo, whose biggest aim is to protect people, can't save them from Tsukishima... and is completely helpless; the poor guy is so freaked out that he wants to kill Tsukishima, something he hesitated to do with Hollows, Arrancars or Shinigami alike. It takes a MASSIVE intervention by Rukia and SEVERAL other Shinigamis to stop him.
As Nodt from the Vandereich has taken leaves outta Tsukishima's books as seen by chapter 501. They invoke the psychic variation implanting needles in your body that warp your mind via manipulation of your survival instincts as well as your conscious mind, and then they use the mundane variation via giving you a Breaking Lecture, so they can finish you. It's as horrible as you think.
Apparently, in Katekyo Hitman Reborn!, all Vongola bosses must go through a 'Vongola trial' to be fit to be mafia bosses where they are put near death to test their resolution. Tsuna was trapped in Hibari's hedgehog box weapon for his trial and was consequently mind raped.
Also, the preferred fighting method of mist specialists, who basically create mental illusions to slowly chip away at their target's sanity. Mukuro Rokudo/Chrome Dokuro are the most proficient at that. In fact, said illusions are so realistic in the victim's mind that they triggered Hibari's allergic reaction to cherry blossoms, can physically incapacitate you until the person creating the illusions decides to let you go (if your mind is not strong enough), and can apparently create pseudo-organs that basically function as normal body parts (as Chrome's missing stomach/intestines, etc).
And recently, Daemon Spade joined the list, by mind-raping Crome ro full obedience, and planning to steal the body of Mukuro.
Happens in Alien Nine, to go along with all of the other horrible things that happen to the cute little girls involved. Doesn't help that one of the characters is (probably) literally raped during the scene as well.
We see that Seimei from Loveless does this to (deep breath) Yoji, Natsuo, Ritsu, Soubi AND his beloved younger brother, Ritsuka. Of course, these are only the people we SEE him mind raping in action. It's implied that there are more victims, not even including the ones that he told Nisei, his subordinate, to do. It's a weird example, because not only does he SEEM display the more "mundane" type, but his unexplained powers can harm people with words, which is usually a Fighter Unit's power, never a Sacrifice's, and he can do so outside of a battle.
Kamen no Maid Guy has Kogarashi's Daydreaming Maid Guy Illusion, which he attempts to use to motivate Fubuki and Naeka to lose weight. He starts by making them believe that their breasts have disappeared, moves on to making them think that they're turning into men, and it only gets worse from there. They're obviously traumatized afterward.
Despite all of the fanservice, Divergence Eve is full of this, not too much on the level of Evangelion, but still some of the stuff that happens in that show is pretty fucked up. Poor Misaki...
Hellsing: This is Zorin Blitz's specialty. In the manga and the 7th OVA she performs a particularly cruel one of these on Seras. She delves deep into Seras's memories, forcing her to relive her painful childhood, where she had to watch her parents be murdered by gangsters and her mother's corpse being raped. While Seras is trapped in the illusion, Zorin hacks off her arm, stabs her through the back, and slices her eyes. She tries this again when Seras is attacking her for murdering and insulting Pip but Seras overcomes it because Pip begged her to suck him dry before he died. Since this was a Last Request, she did it, and it awakened her into a true vampire; she now had Pip's soul within her, and it helped block Zorin's second attempt at Mind Rape.
In episode 6 of Angel Beats! Naoi attempts to use his hypnosis ability to implant fake happy memories into Yuri's mind so that she can disappear. Fortunately for everyone, things don't exactly go as planned.
Done to Hinata in Episode 7 when Naoi hypnotizes him to think he's worse than a clothespin. Surprisingly, Hilarity Ensues.
Naoi attempts to do so again to Hinata in Episode 11, except this time to make him think that he is toilet paper. Fortunately, Otonashi stops him.
Hikitsu from Fushigi Yuugi is revealed to have this as his seishi power. When he removes his Eyepatch of Power, he can make his enemy mentally relive their worse memories... and he can see them as well.
In Gundam Wing, the Zero System causes a Mind Rape effect on whoever is piloting Wing Zero. The technical intention is to show them all the possible outcomes of a battle, but in reality it ends up them horrifying hallucinations that fuck up their minds to different degrees. As an example, when an *already* very unstable Quatre gets a hold of it, he pretty much goes batshit insane until Trowa almost commits suicide to stop him., However, Quatre claims he wasn't even aware of the Zero System, and further claims he never used it as he didn't give a damn about the enhanced cockpit system so much as he did Zero's one-hit colony-killing BFG. (Though this seems to be specific to the dub, but to be fair, the 'golden screens' effect Zero displays when active wasn't seen at all when Quatre first piloted the thing.) ...Now Heero on the other hand, it not only mind raped, it forged some kind of psychic link to the thing since he TALKS to it on at least three occasions! However, he managed to get beyond the madness and make sense of it all. At the time this happened, he was in the Epyon which has the same kind of system, and he was fighting Zechs who was in the Wing Zero. The intensity of the battle managed to push them beyond their mecha's capabilities, and they eventually called a truce and switched mecha. Heero would later get the other pilots to pilot the Wing Zero and find a way to break through as well.
Wufei, on the other hand, uses the damn thing to go on a friggin' vision quest. Better than peyote, or something. (Yes, I know he's Chinese.) His crazy is unrelated.
Sukisho: This is a big central plot theme in the later episodes.
In the RS arc of Pokemon Special, a Magma Elite Mook had the special ability to make people hallucinate with his flames. Ruby was forced to relive his worst memories (good thing that's the one thing that encourages to keep fighting), while Tate and Liza fought illusions to the point of exhaustion (they would have eventually killed themselves if Juan didn't save them offscreen). However, this ability goes straight into horror when he fights Brawly, when it appears that monsters emerging from paintings are grabbing at him and his Pokémon.
In Trinity Blood, Dietrich, who possesses technologically advanced puppet strings that allow him to control a victim's nervous system (meaning, he can control both their senses and their movements), has a scene in the light novels where he basically threatens to do this to Esther by saying that he could make her experience unimaginable agony or the feeling of ten men playing with her body, all while she is unable to move and is being forced by Dietrich to cruelly shoot her comrade in non-lethal areas.
Arguably what happens to Light Yagami when he regains his memories at the end of the Yotsuba Arc. Makes sense, since he was basically forced to watch all of Death Note in the span of thirty seconds. That, and he just remembered killing millions of people.
This happens to Puella Magi Madoka Magica's Madoka, when she got caught in the witch Kirsten's barrier. The witch then uses her powers to torture Madoka by re-playing Mami's death over and over while subjecting her to Body Horror.
Kyuubey is not above doing this. He shows Madoka how the world has been affected by his contracts, and how if it wasn't for the Incubators humanity would probably still be in caves.She did not enjoy it.
Of course, said Mind Rape is to show her why she should become a Magical Girl. She ultimately does, but it backfires on Kyubey spectacularly.
Midnight delivers two to Jellal in quick succession in Fairy Tail, first by taunting him about a past he can't remember, making him out to be the sort of monster that Jellal clearly fears he was, then creating an illusion where Jellal is eaten and then swamped by ghoulish forms of children-presumably children that he used.
In the second half of Tiger & Bunny, Barnaby suffers this twice at the hands of his Parental Substitute, Albert Maverick, who has the power of creating Fake Memories; though it's hinted that it has happened quite a few times prior to the beginning of the series as well. Later, Maverick mindrapes the other heroes via first erasing their memories of Kotetsu, then making them believe he's a murderer.
MÄR: Alviss is the victim of this by Phantom in the Ghost Chess arc.
What Akito Sohma did to Kana in Fruits Basket is a mix of this and More than Mind Control. After Akito blinded Hatori for asking her for permission to marry Kana, she turned against the poor nurse and blamed her so much for Hatori's partial blindness that she drove her mad. It was so bad that Hatori had to delete Kana's memories of their relationship, so effective and cruel Akito's mind rape of her was. We can also count Akito similarly "torturing" Yuki as a kid, telling him he was unwanted and useless every time; poor Yuki was deeply traumatized for years. Also, telling Kyo constantly that he was a monster who could never be loved and should be locked up probably wasn't too helpful either.
It's also stated in the manga that Akito herself was a victim of mind rape at the hands of her own mother, Ren, who told her nonstop that everyone would abandon and hate her ever since she was about five years old. All out of jealousy because Akito was a Daddy's Girl and Ren was jealous of her own daughter, specially after her dad died. This explains, although not justifies, Akito's misogyny and cruelty towards everybody else.
What about Spandam's brutal treatment of Robin in One Piece?
The Marines also preformed a long running Mundane Mind Rape on her. Starting at when she was 8 years old, they managed to utterly convince her over a 20 year period that her mere existence was a sin. Lucky she has Luffy declare war on the world and to say she had value.
Sir Crocodile is a master of this. He's a man who loathes feelings of hope and loyalty amongst those he deems to be weak, believing the weak should know their place against the strong. If he sees said people have these traits, he will do his best to crush those feelings in the most cold and calculating way possible. Made worse by the fact that he is a Manipulative Bastard (of Magnificent Bastard, if you prefer) who prefers his mind rape to be slow and prolonged. He constantly played mind games with Princess Vivi purely for his own amusement, and to stifle her hopes of saving her country. Even to the point where, after making her watch as her soldiers die, and as Crocodile cuts down those important to her, Crocodile holds her by the throat over edge of a high balcony, delivers a Breaking Speech about how all her hopes, dreams, and efforts have not only been useless, but given him more people to kill than he would have if she didn't do anything. Then he drops her. And not by letting her go; by turning his hand to sand, so her struggle to grab his arm to save herself would be in vain. By the end of the Alabasta Arc, Crocodile's cruelty, and the sight of her people killing themselves in a civil war Crocodile orchestrated, finally drove the poor princess to aHeroic BSOD. Fortunately for Vivi, her True Companions are there for her, and Luffy not only catches her mid-fall but he also kicks Crocodile's ass.
the death of Portgas D. Ace.: He dies right before Luffy's eyes to protect him, not fifteen minutes after he has been saved, cuing a Heroic BSOD. It was understandable considering what Luffy had been through to save Ace, most notably fighting in a war far out of league, after having been poisoned until the point of melting, while the cure took ten years of his life. The impact is further enhanced in the anime, as he literaly becomes a colorless husk of a body to show the damage Ace also broke his promise not to die, a promise he made after his other brother died.
In episode 6 of G Gundam, Domon is drugged and forced to watch a holographic re-enaction of his family's downfall by his bosses, to see if he can really use his Super Mode (which is supposed to be powered up through anger-fueled Heroic Resolve). For worse, much later we find out it was all a lie.
Gauron of Full Metal Panic! loves to do this to all of his intended victims. Sousuke seems to be his most consistent target.
Death Note at the end of the series, Near does this to Light. As per stated in his plan to totally defeat him, separate him from all his allies, and rub it in his face. In the manga this is examined in painful detail drawing the psychological trauma in these terms, complete with the unfunny Clothing Damage. Regardless on whether you believe he deserved it or not, it was totally not cool.
Yami Naruto straddles the line between the mundane and psychic. He's a manifestation of all of Naruto's dark emotions and deeply-seated insecurities, and so can dredge up all of his most hated memories and fears, but can only express himself to Naruto verbally.
Orochimaru pulled something like this in the Chuunin Exams on Sasuke and Sakura. By exposing them to his pure Killing Intent, the two of them hallucinated their own bloody deaths, leaving them paralysed in fear.
Berserk gives us another case of mind rape which happened during the Eclipse, one that was much more heinous. Griffith, who is now Femto, forces Guts to watch as he rapes his love Casca to insanity right in front of him. This act is all too similar to Guts' own rape experience as a child: being pinned down and left utterly helpless at the hands of a man who betrayed him, only now he has to see the actual act happen to someone he loves. And the worst part? Griffith might have intentionally done this to torture Guts even more, though Guts had only told one person about his horrible childhood: Casca, who actually helped Guts overcome his trauma. Meaning that Griffith might have some omniscience that saw into Guts' Achilles' Heel. It's no wonder that Guts wants Griffith dead with every fiber of his being now.
In Pandora Hearts, Jack Vessalius does this extremely effectively to Oz by showing him immensely traumatizing memories from his forgotten past, including the memories of being forced to kill countless innocent people as the B-rabbit despite not wanting to. Jack finishes off by telling Oz, "You've never really had anything to call your own, anyway. Don't forget that..."
Not to mention all that crazy stuff that happens to Alice early on in the series, such as the Will of the Abyss trying to break her by talking and her less-than-pleasant memory fragments that haunt her in Cheshire's dimension.