In the doujinshi Besame Mucho, Spain gets one of these (quoting the trope name included) when standing in front of a destroyed house in a village his army just slaugtered. He is passing by when he sees a dead child's arm peeking out of a pile of wreck, and it makes him remember about Romano. Something was in my eye when he says that they just killed people, who were the same as him or little Romano. His companion's answer? "You are wrong. You are not human.". Tear Jerker, indeed.
Also in an Axis Powers Hetalia fic, this is lampshaded by an authoress in the notes of the first chapter of her intense FACE bondage-dominance foursome. Repeat, the /first/ chapter.
In yet another Axis Powers Hetalia fanfiction Let me be Your Savior Romano/Lovino has one after stumbling across his brother (Italy/Feliciano) after Romano/Lovino had violently raped him crying, and it finally hits him that what he's been doing is wrong. This scene is a nice breakthrough, seeing as Romano/Lovino had seemed to cross Moral Event Horizon before.
Just about every fan-written sequel for the controversial Kink Meme story known as the Financial Crisis Gangrape has America's attackers all go through this in varying degrees. Depending on how forgiving or vindictive the individual author is, at least one of the rapist nations either gets Driven to Suicide from their guilt or suffer a massive BSOD.
Multiple examples in Soviet Insanity. In particular, Belarus when she stabs Lithuania and Russia once he realizes the extent of the psychological damage he has inflicted on his family.
Xander has two in Emerald Dawn. The first when he realizes one of the kids he shot with an arrow on Halloween died. The second when he overhears demons talking about the Robin Hood type hunter going around killing every demon he sees, including a young couple who left behind a three year old orphan.
Almost every (if not every) Five Nights at Freddy's fanfic involving the animatronics being good-hearted and realizing that they've been killing people when they stuff them into animatronic suits (not helping exoskeletons get into costume) uses this trope.
In the Jackie Chan Adventures and Teen Titans crossover fanfiction A Shadow Of The Titans, Jade has a reaction like this when she severely wounds Kitten during their battle in the Tournament of Villainesses (to be fair, not only was Kitten reallyrude to Jade when she was severely outclassed and offered a chance to surrender, Jade, due to her previous encounters with the Titans, etc., expected her to be Made of Iron). Of course, the other villains think her reaction means something else.
Fluttershy has this reaction in chapter 10 of Ace Combat: The Equestrian War. She saved Cloud Kicker's life, but believes her actions partially led to Razor's death. She utters the actual quote (without the "My God" part) and until her friends comfort her later on, along with Princess Celestia stating that Razor died in the explosion caused by The Burning Talon's overheating, she is reduced to cryingand blaming herself.
Twilight has a mild one after killing a Dalek, if only because she had previously thought it was an robot instead of a living creature.
Rainbow Dash has one when she realises that her Buccaneer Blaze tore Pikachuto shreds - she had been ready to kill in self defence, but she hadn't meant to be quite so brutal.
Pinkie Pie has one after beating Taokaka, as the two had gotten on well up until Discord showed up with a horribly inaccurate video of her battle with Lucy.
In Origins, a Mass Effect/Star Wars/Borderlands/HaloMassive Multiplayer Crossover, Sarah has one for a relatively minor reason (all previous actions considered) when she loses it over the fact that Jackie's reform has been accepted but everyone is (rightfully) suspicious of her. Giving in to her darker impulses, Sarah attacks Jackie, only to break down crying and use her powers to try to undo what she'd done all while chanting "I need help."
In the Lilo & Stitch/Star Trek crossover Starlight, Jumba undergoes this thrice: first after he loses Lilo to the Borg, then after he accidentally leaves Experiment 426 behind to be apparently flung into outer space, and lastly after he shocks BorgDrone!Lilo to knock her out, during which she writhes in agony.
Luna in The God Empress of Ponykind has a moment like this after the war against the Crystal Kingdom, when she realizes that she was about to betray her sister. Unfortunately for her, The Corruption takes over her immediately after this.
Mordin Solus has a truly tragic case in Harry Potter: Geth when he sees Mount Mordin: a massive pile of all the Krogan babies that died after he modified the Genophage to be more effective. It's stated as containing roughly a hundred-twenty million corpses. Jack is horrified and Samara openly states she would kill Mordin if she wasn't under oath.
In Graduate Meeting Of Mutual Killing, has one of these in a flashback. It's shown that Ginchiyo, when she received the letter from Hope's Peak, tried to leave her sister out of the school and pass herself as the receiver of the letter, just to be told that the offer was for both her and her sister. She then hurried back home to tell her, and finds out her sister ran away from home in despair. Ginchiyo tries to atone for years, looking for her sister, and before the Filmmaker's death, she states she believes her sister is dead, as she couldn't find her.
In Despair's Last Resort, Shizuka Matsuki has one of these upon realizing that she's caused Naomi's death and actively killed Shigeru, and that if she graduates then those actions will be for nothing.
In the Tamers Forever Series, when Chaos first emerges, but before Takato realizes he's a separate entity. From his perspective, he destroyed a significant part of the Internet just by having his Berserk Button pressed. You'd be a bit scared of yourself too.
This is also Takato's reaction when he uses the Omnivice to remove the pain from Azulongmon's Wind Electricity technique, only to find out that he'd transferred the pain to Rika, Henry, Renamon and Terriermon. His horror, frustration and grief combine to send him over the edge, unleashing the power of ChaosGallantmon.
In The New Retcons, after Elly snaps out of her insanity and is confronted by the doctors with what happened to her and what she did to others, she's horrified at her actions, particularly when she reads the letters she wrote while insane, and realizes how much Connie enabled her.
In The Day He Was Pushed Too Far Dumbledore, in order to avoid legal repercussions, lets a copy of Harry "die" and gives Harry a new identity after Harry shoots Umbridge and then himself fifth year. Harry says "What have I done?" shortly after coming across Neville, who's been dealing poorly with the "loss" of the only person who cared about him, trying to kill himself.
In Lily's Changes Voldemort says this almost word for word after eleven-year-old Harry, having future knowledge, convinces him to absorb the soul fragments in two of his Horcruxes, regaining his sanity.
Percy Weasley has this reaction in Fixing What Has Been Broken after he learns that James Potter kidnapped Harry from the Saint Mungo's nursery when the real Harry Potter died shortly after birth and consequently he'd been vilifying his own brother.
In Exfriends, Lovers and Brothers Ron, upset about Harry being gay, punches him in the stomach. He has this reaction after learning that he caused Harry to lose his unborn child.
In Maim de Maim, Nui gets two of these, one is from when she skinned a girl alive to make a kamui and another is after Ryuuko and Senketsu are brainwashed. Ragyou appears to have one in chapter 22 when she shows and appears to be feeling a twinge of regret, during one of the few times she shows genuine emotion.
In Cellar Secrets, we have this with Ragyou over what the abuse she's put her daughter (especially Ryuuko, to whom she locked in the titular cellar) and secretary through when Satsuki visits her in the mental asylum.
Ragyou (articulating her regret): "I danced with the devil and I'm so ashamed."
Sora in Broken Heroes has this reaction twice: When Ventus dies and he realizes how much of a Jerk Ass he has been to him, which causes his character 180, and when he agrees to become Xemnas's slave (Implied to be Sex Slave) to keep Riku, Kairi, and his other friends safe, which spurs him into adopting the identity of Roxas.
In The Times They Are A-Changin', Zoe is "horrified and ashamed of herself" after she gives Pepper an Eye Scream injury during a fight. She doesn't protest when Mrs. Twombly isolates her from the other pets, since she considers it "an appropriate punishment".
In Left, Frodo has two of these. One happens during a dream sequence when he discovers that he killed Sam in a fit of Ring-jealousy. The other happens when he lashes out at Sam in Cirith Ungol and realizes how close he came to fulfilling the nightmare.
In Maternal Instinct (MLP), in a fit of unbridled rage, Queen Chrysalis exploded in a vicious tirade against her heavily mentally and physically disabled daughter and heir, Princess Pupa and proceeded to beat her. Savagely. But when Chrysalis came to her senses and saw her daughter on the floor, barely conscious and with blooding oozing out from wounds on her crown and temple, the aghast and repentant Queen immediately threw herself at her daughter's mangled form, kissing her face and trying to stop the bleeding, mentally crying, ‘Kami above, forgive me! Please, forgive me!’note You may have been able to tell, but.. yeah, this is seemingly meant to parallel Ivan the Terrible.
After The Gala shows this as Fluttershy's reaction to her explosive display of anger at the Gala. She's outright horrified by what she did and left a sobbing wreck. Her friends console her, though, and manage to get her out of her Heroic BSOD both by their forgiveness and Celestia revealing everyone was okay and it wasn't entirely her fault (the animals were rather wild to begin with and Celestia apologises for not warning her beforehand).
"I do not need to be told the heinous nature of my actions!"
Subverted, however, because the author doesn't portray her as being entirely in the wrong for taking said actions. For those not familiar with the story, Celestia has been forced to separate a young filly from her adoptive mother -hopefully temporarily- in order to perform a complex diagnostic spell on her, acting against her better judgement but on the advice of an expert in the dangerous form of magic that the filly in question had been touched by. This would have been unpleasant but justifiable, save for the fact that Celestia did not find out that the person giving her that expert advice was being economical with the truth to further his own agenda until the hit the fan.
The spy Lord Eminence in Under The Northern Lights when he realizes that his plot has been found out because he has been very careless because his special talent for being inobtrusive and even turning invisible doesn't work on reindeer, meaning there are lots of witnesses to his acts. He acted alone, convinced his success would force his superiors to accept a job well done, but Princess Luna is not only against the plan per se, she is also furious that he was so careless as to be found out. He doesn't say the actual phrase, but falls to the floor and moans "Mare in the Moon!" which prompts Luna to chastize him further for taking her name in vain when she is standing right there.
Twilight has a few of these as she copes with the fallout from Hard Reset. Especially given how she started treating ponies (herself included) during the "Groundhog Day" Loop.
According to A Brief History of Equestria, this was Smart Cookie's reaction when she realized that the plans she helped Puddinghead draw up for colonizing a new homeland would mean effectively leaving the other tribes to slow death by starvation and hypothermia.
In Equestria: A History Revealed, after the climactic battle of the Equestrian Civil War, Princess Luna finally realizes the extent of what she had done, and then suffers from a Villainous BSOD. This conflict in her heart acts as the catalyst to allow the Nightmare forces to possess her body and complete her transformation into Nightmare Moon.
A Future of Friendship, A History of Hate: Rarity has this reaction in Episode 4 when she realizes that she's been blowing off her friends without a thought in order to spend time with Regal Rule, most prominent being that she completely forgot about Fluttershy's birthday.
Spitfire has this reaction in the Reading Rainbowverse when she realizes how horrible she's been to her daughter.
Celestia reacts this way after she learns what she's inadvertently caused Navarone to become in Diaries of a Madman. Nav himself also shows this, when he sees first hand how cruel his suggestion for feeding the changelings is.
In Zenith, Celestia has this reaction when she finds out that her decision in letting Spike stay with Twilight rather than having him go back to Ponyville only made things even worse for him.
A Taste of the Good Life, from the same author as Hard Reset, has this twice over in the aftermath of a climactic scene midway through the story. Scootaloo's mother, Ebony Glimmer, is hanging for her life off a cliff and the only pony around who can help her is Scootaloo; the pony to whom she'd been an emotionally abusive drunk, forcing the filly to run away. Scootaloo had said, repeatedly and clearly in the last few moments alone that she wanted nothing to do with Ebony, especially after Ebby used Foal Protection Services to essentially steal her from the ponies she loved in Ponyville. Scootaloo walks away, prepared to let Ebony fall and die because it would means she'd go away forever. Ebony is saved, but in the aftermath Scootaloo is horrified by what she had been prepared to do and Ebby comes to a Heel Realization about how she had been acting towards Scootaloo.
The Witch of the Everfree: Applejack gets snapped out of her blind rage at the Great White Wolf for killing her parents when seeing Sunset Shimmer slowly killing it for her. Her reaction in turn causes a milder one in Sunset, who then finishes it off quickly.
A Mother's Love: Fire and Blood: The Third Hokage for pretty much screwing Kushina and Naruto over (The Third made it so their lives would be miserable) and letting them get kicked out of the village. The village has one years later when they admit that kicking out them out was a dick move on their part since ''The fox in the desert'' might return for revenge.
Sasuke gets one in NBH when she gets captured after trying to defect to Sound. Not only does she has no hope of killing Itachi anymore (even if she was allowed to remain a ninja, Ino destroyed her Achilles tendons), but she once more lost everything; this time because she threw it all away herself.
In Echoes, Kazama has one after he burns down most of Konoha, and realizes that while he got his revenge on the Inner Council, he had hurt thousands of people who didn't even know him, on top of his friends in the Konoha 12, several of which he killed.
In Vapors, because she is a self-insert original character into the Naruto world, Aiko holds herself responsible for every bad thing that happens in the story. Tsunade also has one of these, when she realizes that giving Aiko insufficient support during her mission to infiltrate Root, followed by handing her a student who would be at risk from Danzo, put Aiko in a position where she had to kill one of her teammates in cold blood, despite the man trusting her to help him.
Kurama has one in Played to Death when he realizes how much going along with Naruto's idea to make videogames real has damaged the boy. As he explains to Hana, he can barely get the boy to go outside as Naruto honestly prefers being in places where everything is trying to kill him to being in the village. As a result, Kurama outright begs Hana to give Naruto something, anything, to live for.
Asuka, who has been physically and sexually brutalizing Shinji for months, has minor moments of this whenever her temper finally abates, then has a massive moment of this coupled with Villainous Breakdown when she finally beats Shinji badly enough to nearly kill him. The fic starts after this moment; when it's not filling in backstory, it's detailing her attempts to atone for her actions.
Shinji, on the other hand, blames himself for everything Asuka has done to him, seeing his actions during the canon story (especially the hospital scene in Eo E) as so unforgivable that he can justify her abuse as karmic retribution.
In Saki After Story, Teru viciously attacks her younger sister Saki while denying that they're related, as well as Nodoka when she comes to help, injuring them badly enough to put them in the hospital. After her teammates run in and stop her, Sumire tells Teru that she knows that Saki is Teru's sister, and what Teru did to her and Nodoka is inexcusable. Teru says the following quote before she's arrested, both in reference to beating Saki up and for refusing to acknowledge her as her sister.
In Episode 74 of Sonic X: Dark Chaos, Tsali's core systems are damaged in the previous Episode, causing his programming to become scrambled. Because of this, the programs preventing him from feeling regret or remorse for his crimes are disabled. When he and the heroes find out Maledict had been manipulating him from the beginning, he completely breaks down into a sobbing wreck as his systems starts going into full Logic Bomb meltdown - and the horrors he unleashed come back to him.
Knuckles has one of these at the end of Episode 73 after setting Tails on fire to destroy his Shroud form, and nearly burning Tails to death when it changes him back to normal.
In chapter 82 of Gensokyo 20XXV, it was noted that, after she stabbed Yume Ni with a pair of scissors in a fit of rage, Reimu expressed remorse for her actions, recognizing it as something she shouldn't have done.
Earlier in the series, 20XXI, Ran and Kanako have both have this at different times. Ran has this when Reimu takes a horrible fall and loses the function of her legs while she was being negligent, while Kanako has this when she thinks she may have caused Sanae's death, after having been abusing her for some time.
In Cenotaph Taylor seeks revenge on Bakuda and the greater ABB for murdering her father. Over the course of an arc and a half she carefully tracks Lung and Bakuda down, then sets off Bakuda's own grenades in her workshop with both Lung and Bakuda in the blast radius. Little did did she know- Bakuda built in a deadman switch tied into several thousand bombs implanted in both gangmembers and kidnapped civilians in the event she was killed. Taylor dosen't find out until the next day, while enjoying a social breakfast with 'James' and Lisa. She... dosen't take it well.