Sayaka from Puella Magi Madoka Magica has this reaction when she makes Madoka cry after she yells at her for not using her latent power to fight witches. Unfortunately, this realization helps push her towards the Despair Event Horizon and she becomes a witch.
Not to mention Madoka herself had this reaction two episodes prior, after throwing Sayaka's Soul Gem off a bridge and onto a moving truck to keep her out of a fight only to find out that said Soul Gem literally contains Sayaka's soul, and by throwing it away she almost killed Sayaka.
Robin Mask suffers from this when he thinks he's killed Kinnikuman during their fight in the 20th Choujin Olympics. Especially noteworthy in that Robin was previously in an Unstoppable Rage- once it wears off, he realizes that he was taking the fight to seriously. While he's lamenting, Kinnikuman puts him in a finishing hold, winning the match.
Dragon Ball Z: Vegeta had this twice, once when he allowed Perfect Cell to reach his perfect form and again when he allowed Majin Buu to resurrect.
Gohan had this too, thanks to his cockiness.
A short while before the above example, Goku had one of these moments on his own when Piccolo reminded him that Gohan was partially human, didn't share Goku's lust for battle, and thus didn't find any pleasure at all in getting curbstomped by Cell while his father simply looked on from a distance.
In the Buu saga, Piccolo tells Super Buu to kill the people of Earth, hoping that it will stall him and intending to wish back everyone with the Dragon Balls later. However, Buu then fires the Human Extinction Attack and kills everyone in the world in less than three minutes, leading Piccolo to have this moment.
In the OVA of Angel Sanctuary, Katan says this while looking down at his hands in horror after accidentally killing Sara, when he was actually aiming for Setsuna.
Magical Project S Misao Amano (as her evilMagical Girl alter ego Pixy Misa) was destroying the city and almost killed her only friend Sammy and her parents, to the point where she ran away due to guilt, this was justified although it was her other personality did this and was unaware of what she did. The twist here was that what she did was realy her (her repressed aspects,) and not brainwashing.
Guld Bowman In Macross Plus gets a simultaneous double helping of this, when he finally overcomes his Trauma Induced Amnesia in the middle of a Macross Missile Massacre which he believes has killed Isamu Dyson, the person who he had blamed for the trauma. Actually caused by his own attempted rape of Myung, a memory he had suppressed until that moment.
For a villainous example, in the 3rd Naruto film (Guardians of the Crescent Moon Kingdom) the baddy Ishidate accidentally turns his employer—and more importantly, paymaster—to stone. Oh Crap.
Sakura has this reaction when she realizes what the promise she got out of Naruto did to him.
Yamaki of Digimon Tamers actually yells this under the dramatic and appropriately messed-up sky created by his program Juggernaut, an attempt to purge digital life from reality that instead results in a massive and highly dangerous breach between the worlds. Of course, this a fellow about whom the line, "Looks like your pal Yamaki ripped open the sky again," has been uttered. This of course leads to him being fired, and after a good sulk, he begins his Heel Face Turn.
Beelzemon spends a good deal of time wandering the Digital World listlessly, thinking back over his actions after he kills Leomon and is later saved by Leomon's Tamer, Jeri. He's so disgusted by himself that he completely loses the will to fight and even to live, not even trying to fight back while a group of Chrysalismon beat him halfway to death. He (somewhat) snaps out of it when he finds out that Renamon and Rika risked their lives to find him, and, well...I think you knowwhere this is going.
And another one after his EVA nearly kills Toji Suzuhara due to his inability to fight. This haunts him to a greater degree in the manga since he actually kills Toji, and Kaji tells him to take accountability because he didn't try harder to save him, just standing by until his father activated the Dummy Plug
In the third Rebuild of Evangelion movie, Shinji has not one, but three such moments - First, when Kaworu shows him the devastation caused when he inadvertedly set off the apocalypse in a desperate attempt to save his de-facto girlfriend during the climax of the previous movie. Next, word-for-word, when he realizes that, on top of that, it was completely for naught since the girl in question is still dead and what he thought was her is just a clone of hers, which tears away the only coping mechanism he had. The third time occurs when he sets out to atone for this and sets out to Set Right What Once Went Wrong. Except, the Reset Buttonis a lie, and all the supposed "Spears of Hope" will do is to blow the pathetic remainder of humanity to hell. As he sees the destruction begin around him, he reacts with utter mortification. Needless to say, by the time that movie is over, he's reduced to a near-catatonic shell, mad with grief and guilt. And the poor thing is only fourteen.
Renton from Eureka Seven does this after he goes berserk and tears an army of enemy LFO's to shreds. He doesn't really have enough time to ask of God what he has done. He, instead, loses his lunch over the debacle.
The impact of this cannot be fully felt if you don't realize that up until this moment Renton (and many members of the audience) didn't realize that the entire time he's been fighting enemy LFO's, he's been killing people. He simply thought that enemy LFO's were robots.
Lelouch from Code Geass has a Delayed Reaction version of this when the memory of his murder of his half-brother Clovis from the previous episode causes him to vomit (you see the bathroom sink water running indicating he did get sick).
Suzaku also has one of these when he realizes he's Jumping Off the Slippery Slope by trying to drug Kallen to get information out of her. Followed by Nina Einstein, once she witnesses the horrendous results of her FLEJIYA nuke.
Lelouch actually has another one of these, when he loses control of Geass and Euphemia gets hit with his off the cuff command to KILL ALL JAPANESE PEOPLE! The look of utter shock on his face spoke volumes.
Earlier in the series, he gets a similar expression upon being informed that his love interest's father was among the casualties of his latest battle. Although this isn't as objectively big as the aforementioned incident, it shook Lelouch rather badly and forced him to personally face the consequences of his actions and orders.
Darlton gets one of these after his hypnosis wears off and he realizes he just saved Zero by shooting Cornelia in the back.
Mikoto from Mai-HiME breaks down when she realizes she was responsible for killing her best friend Mai's brother Takumi... and her own grandfather.
Shizuru also gets a slightly more understated one after her resurrection in the Grand Finale, crying openly over the fact she'd forced her lesbian crush into a Taking You with Me situation because she'd gone out of control. Not as severe as some, but given Shizuru's graceful serenity over the entire series to that point, seeing her outright crying and apologizing through the tears had impact.
Yukino after she is blackmailed into trying to kill Mai. Even after the almost victim later thanks her for helping her find Takumi, she still feels quite guilty.
In Mai-Otome 0~S.ifr~, Elliot has this reaction after trying to kill Sifr on Una's orders, thus resulting in Lena being forced to block an attack, leaving her open to M9, and Lena is eventually defeated after overloading her gem. After seeing her in tears over it, her companions forgive her, although Sifr asks if everyone, having withheld information from her all along, wants her dead.
The protagonist from Tsukihime goes through this in every route, after he regains control/consciousness from whatever insanity/inversion/dream-turned-reality he just went through, all of which generally involve him causing bloodshed and death.
Gyoubu Kasumi from Basilisk, after Tenzen grabs a flautist boy and throws him into the middle of their fight, causing Gyoubu to accidentally kill the boy's father when the old man tries to save his son.
In Yu-Gi-Oh! Duel Monsters, season 4. Yami in a big way after that Raphael duel - youknowtheone. In an attempt to win, he plays the Seal of Orichalcos, and when he loses, Yugi offers his soul instead.
Mai, when she snaps out of the Orichalcos' control.
Noah, in the virtual world filler ark in the anime, about 3 seconds after he enters a helicopter to escape from the nuke he sent himself to destroy the place.
Saji Crossroad in Mobile Suit Gundam 00after realizing that his cowardice began a chain of events that resulted in a group of resistance fighters and helpless refugees being massacred at the hands of the ruthless A-LAWS.
Happens quite often in Detective Conan, probably the most memorable one being a case of a murdered rock star who was poisoned during a little get together. When it's revealed that one of the band mates, who happened to be an jilted ex-girlfriend of his, was the murderer. One of her friends points out that the singer still loved her and reveals so through a postcard with song on the back dedicated to her. The woman breaks down at once she realizes her own foolish action.
While the girlfriend breaks down crying and screaming Conan gives the memorable quote 'When people build walls around their hearts all that can come out of it is pain and suffering.' It might have nothing to do with the trope but it was in the same episode.
Doctor Marcoh from Fullmetal Alchemist. Now that he's gone and made the damn Philosopher's Stone already, he feels horrible about it. With good reason. Also, most of the protagonists in the Ishval arc. War suddenly doesn't seem so great anymore.
Edward Elric, in an attempt to bring his mother back to life, ends up losing his arm and leg and nearly bleeds to death, his brother's body is completely destroyed and he ends up as a soul in a suit of armor, and then he realizes all he managed to do was create a writhing mass of nightmare fuel instead of his mother. He really could have used some therapy.
When Greed kills his only surviving True Companion after being Mind Wiped. Big "NO!" ensues.
In the manga Pokémon Special, Ruby does this when he realizes he was a huge Jerkass to his Feebas after she loses a Contest and caused her to run away. He only partly realized that on his own at best, and it takes a tongue-lashing from Wallace before it finally gets through to him completely.
In the Asatte No Houkou manga, Amino has this reaction when he finally realizes his actions hurt Karada.
Shown in Tsubasa Reservoir Chronicle. While not actually said out loud, it is spoken perfectly clear by the look on C!Syaoran's face when he looks down at what's left of his loved one, C!Sakura, who he accidentally impaled.
Fai during the Infinity arc is forced to kill Sakura thanks to his first curse. He then proceeds to lose control of his magic, tear up the arena around him, and nearly commits suicide. It gets worse.
Bleach: Hitsugaya has this when he and the others attack Aizen and believe that they succeeded, only for the illusion to drop and reveal that Hitsugaya has quite literally stabbed Hinamori in the back.
Kira has this reaction after he learns the truth about Aizen's plot, including that his friend Hinamori is in critical condition. He presumably was merely following Ichimaru's orders, and noted that he promised that Hinamori wouldn't get hurt.
Urahara in the "Turn Back The Pendulum Arc" when he realizes that he sent Hiyori into a dangerous situation all alone.
Don Kanonji when he learns that he had been turning ghosts into Hollows when he thought his exorcism technique had been sending them to Heaven.
And Ichigo when he finds that he stabbed Uryu while possessed by a Hollow. Of course, this is cut short when he finds that Ulquiorra is dying as well.
Bisco Hatori's Millennium Snow has the vampire male protagonist, do this after he grazes Chiyuiki's neck with his fangs, meaning she will have to live for a thousand years with him also counts as a What the Hell, Hero? moment, as Satsuki promptly tries to kick his ass afterward.
Mayo Sakaki in the 3rd Fushigi Yuugi OVA. When she realizes that her behavior is destroying the universe (and herself), and that love and obsession aren't the same after talking with Houki, she is Driven to Suicide and attempts to drown herself, believing herself to be beyond redemption.
In the novel, Last Order claims that Accelerator never liked the killing of 10,000 sisters experiment in the first place and the reason why he acts so cruel to them is to discourage the remaining sisters from going after him.
A Certain Scientific Railgun. Kiyama Harumi has this, after the subjects of one of the experiments she participated in (children in her school class) fell into comas and the head scientist of this program put a gag order in effect and was more concerned about the data then about the children. Later, she found put that the experiment was deliberately dangerous.
In JoJo's Bizarre Adventure Part 2, Strohiem has this reaction once the "Ultimate Life Form" (Satanna) escapes from what he thought was an inescapable cell, and proceeds to start slaughtering every single Nazi in the base.
The title character of Nadia: The Secret of Blue Water has a look like this toward the end of Episode 20, after taking a bath with Electra where she learns that she had misunderstood Jean's friendship with Electra. Earlier, she had been quite nasty to Jean (in a fit of jealousy) when he attempted to compliment her (as advised by Electra). She later learns that Electra only considers Jean as a brother, and feels quite remorseful for her hair trigger outburst at him. (The same is true in that episode when she realizes, again from her talk with Electra, that she has misjudged Nemo and the Nautilus.)
In the final episode of Tenshi Ni Narumon, after Silky sets their wings on fire, Mikael snaps out of his madness and when Raphael appears before him and confronts him with what his actions have led to, Mikael breaks into tears, expresses his remorse over what he has done and pleads his teacher to rescue everyone. When Raphael disappears, Mikael just resigns to the worst.
In the movie version of Magical Girl Lyrical Nanoha, Precia gets one over how she had treated Fate when she remembered that Alicia had always wanted a little sister. Unfortunately, by the time she remembers this, it's too late to apologize or make amends.
Van Argeno from Blood+ when he witnesses the results of his research turn members of the public into Chiropterans.
Keito Nichi in Star Driver when she realizes that by trying to manipulate and backstab Head, she has actually doomed Sugata to either death or eternity as Head's slave. She was trying to make it so he could rule the world out of her love for him.
In Monster, after seeing all of the death and despair caused by Johan Liebert, Franz Bonaparta breaks down completely, feeling guilt for being the man who made Johan into the monster that he is.
Windaria Izu/Alan when he realizes the magnitude of what he's done by flooding Itha/Lunaria and how many lives he destroyed.
Jinbe from One Piece expressed guilt for letting his hatred for humans get the best of him and he wound up indirectly letting Arlong to go to East Blue and terrorize Nami's village for years. He felt quite ashamed of this and offered to accept any punishment Nami wanted to give him.
Can also apply to Ian when Jeremy finds the pictures Greg took of him after whipping/raping him that Ian kept. Jeremy, as expected, reacts negatively and has a Freak Out , which leads to Ian's What Have I Done .
In Black Lagoon, Roberta reacts like this after she blasts GARCIA, of all people, in an instinctive trigger-pull near the end of El Baile de la Muerte.
In Gundam Wing, Heero is overcome with this after destroying an airplane carrying what he believed to be senior members of the OZ organization. Then Wufei arrives and tells them that he just actually killed all of the senior leaders of the United Earth Sphere Alliance who wanted to make peace with the space colonies. It was then everyone realizes they'd just been suckered into Magnificent Bastard Treize's Batman Gambit; it was also then when they realized this was not a black-and-white war.
In Say I Love You, Yamato starts to realize this when Aiko calls him out on the rumor that he was seen leaving Megumi's apartment. She tells him that Mei, his girlfriend, was deeply hurt by that rumor. He initially doesn't think there's anything wrong with it, since he states there's nothing going on between them, and he's simply going there for dinner. Aiko then asks him that if the situation were reversed, where Mei was going to another guy's house without his knowledge, if Yamato would be okay with that. He runs off and begins searching for Mei, canceling his photo shoot with Megumi in the process.
Hiyori of Kotoura-san suffers this after she arranges for thugs to beat up Manabe for choosing Haruka over her. The encounter doesn't go as planned, ending up with Manabe getting injured - stabbed in the manga and sorely beaten in the anime - and sent to the hospital. She then suffers Heel Realization about how much of a Jerkass she's been.
For the same incident, Haruka also believes she's the cause of all the strife between Manabe and Hiyori for the latter's jealousy.