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 than about the children. Later, she found put that the experiment was deliberately dangerous.
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 My God, What Have I Done?.]
In Assassination Classroom Terasaka is utterly horrified after seeing that he unknowingly put his classmates in jeopardy. The anger that drove him to work with Itona and his handler instantly evaporates and he briefly goes into denial, only to be slapped out of it by Karma.
In the Asatte no Houkou manga, Amino has this reaction when he finally realizes his actions hurt Karada.
Jean is horrified by his own actions, after successfully leading the other trainees to safety. Not only did people die on his command trying to reach headquarters, but he intentionally used the deaths of other comrades to pull the whole thing off.
Titan agent Annie is so horrified by the aftermath of the attack on Trost that she can only stand there in shock, apologizing to what might have been her friend's corpse.
In stark contrast to the previous two, Bertolt, the third Titan agent, initially shows no remorse for his actions. Even being reminded by Eren that he is directly responsible for Eren's mother's death (a piece of the Wall he kicked crushed her legs so she couldn't escape the Titans) garners no emotional reaction from him beyond admitted pity. Later, when confronted by the rest of his former squadron comrades, he breaks down and admits he hates what he's done and did come to care for his friends.
Both Levi and Hange experience a brief moment of this when they find out Titans are actually transformed humans.
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.
Berserk: Guts, when he kills Adonis, a young child, after Adonis saw him murder Lord Julius.
Griffith, when Ubik shows him all the people who died, either by Griffith's own hands or due to his machinations, in his quest to obtain the castle he dreamed of. Unfortunately, this doesn't last, and Griffith goes from apologizing profusely and begging for forgiveness to the realization that he's too far gone to feel regret or remorse for his sins, and resolves instead to kick it into overdrive.
Later, Guts nearly raped Casca and bit her in the process. From that point on, he began to keep his distance from her while she kept hers.
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.
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.
Van Argeno from Blood+ when he witnesses the results of his research turn members of the public into Chiropterans.
The manga version of Chrono Crusade has Chrono do this after his Unstoppable Rage in volume 5. He's so distraught he can't even quite get out the words: "Oh, no. Have I done? Ro...sette!"
Lelouch 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.
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.
Digimon Fusion: Much like Ken, Ewan Amano didn't realize Digimon were living creatures until his battle with Taiki. He also makes a Heel–Face Turn, though it takes until the sequel for him to earn his partner back.
Yamaki 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.
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.
Vegeta after Future Trunks gets murdered by Cell. He realizes he's neglected his own son and goes on a Roaring Rampage of Revenge.
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.
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.
Happens to Caster in Fate/Zero when he sees the light from Saber's Excalibur. It reminds him of the joy he felt when he was with his beloved Jeanne and the latter's purity, and he manages to muster out "What... have... I..." before being killed.
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.
For Edward, Al, and Izumi the greatest horror after their failed human transmutations was the thought that they had brought their loved one back only for them to die in agony again. The discovery that the humans they transmuted were soulless and not even similar to the loved one frees them from lingering guilt.
From the same continuity, Roy after killing Winry's parents.
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 High School D×D, Lord Zeoticus Gremory has a moment upon realizing that he was forcing his beliefs onto his daughter Rias, such as organizing an Arranged Marriage to Riser Phenex as opposed to letting Rias choose a husband for herself when Riser was really a major jerkass and Rias is against the marriage proposal. Zeoticus's son Sirzechs helps Rias's Love Interest Issei Hyoudou defeat Riser in an Engagement Challenge; Zeoticus apologizes to Lord Phenex for her cancelling the engagement and he is Easily Forgiven. It's even lampshaded by Zeoticus's wife Venelana in Volume 5.
Kill la Kill: Ryuko has this when she ends up stabbing Mako while being controlled by Ragyo. The shock of it is enough to undo the brainwashing.
In Mobile Suit 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 Happiness Charge Pretty Cure, Iona Hikawa/Cure Fortune spent half of the series giving Hime Shirayuki/Cure Princess hell over her Dark Secret, opening the Axia Box and letting the Phantom Empire free. Because of it, Iona's sister, Maria/Cure Tender, was defeated and captured by Phantom. When Iona finally confronts and battles Phantom, Phantom easily overpowers her and destroys her PreCards before revealing the truth - Maria's defeat and capture wasn't Hime's fault, it was Iona's: she wandered into the fight between Maria and Phantom and when Phantom targeted Iona, Maria took the hit meant for her. Iona doesn't take it too well. She gets another one when Hime finally gives her her reasoning for what she did - she was tricked into opening it after hearing a sad voice from inside.
In Higurashi: When They Cry, several of the characters have these moments. Heck, Keichi has two regarding the same horrific event.
Shion even wets herself upon hers.
That may be a very, very different kind of wet for all we know.
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.
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.
Hiyori 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.
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.
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.
Mikoto 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.
In the second volume, when Taishou realizes that he allowed his jealousy of Fukami working on a project with his best friend Buchi, he lets his anger get the better of him and he ends up raping Buchi. After coming to from a punch from Fukami, Taishou realized what he has done and he breaks down crying.
In the fifth volume, Fukami ends up raping Buchi because he developed feelings for him and he was going to admit his feelings for him, but his mother abandons him which causes him to become lonely and he feels that Buchi wants to be raped like back when Taishou raped him. But on the morning after he rapes Buchi, he to immediately regrets what he ha done when he sees Buchi.
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.
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 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.
In episode 7 of StrikerS, Teana's recklessness almost ends up getting her best friend Subaru hit by friendly fire (fortunately, Vita was able to intercept it with Graf Eisen). The entire time that Vita's scolding her she's paralyzed with guilt, and at the end of the episode she breaks down into tears. Even worse, she ended up making the same mistake the next episode during the "White Devil Incident", causing her to have this reaction again in episode 9.
Subverted in ViVid Strike!. Rinne was initially horrified when she sent three girls who had been viciously bullying her to the hospital. Then she found out that the girls lied to their families and claimed she attacked them unprovoked, at which point any guilt she felt disappeared.
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.
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.
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.)
The Fourth Kazekage's reaction to seeing Gaara as a sane, Wise Beyond His Years shinobi who is now Kazekage and the Commander of an entire army of ninja from across the globe, finally realizing how much of an idiot he's been. Ironically, this only happened after his death, via the Edo Tensei.
For a villainous example, in the 3rd 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.
Shinji Ikari has such a moment 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
He has another that pushes him into a Heroic B.S.O.D. after he is forced to kill the angel Kaworu.
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 teammate 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. 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.
In the Skypiea arc, more specifically Wyper's flashback: Calgara and his village begin acting coldly towards Noland after he cuts down a great many of their trees, which they believed their ancestors to be in. This is after Noland saved them from a plague and they threw a party on his behalf. When Calgara's daughter learns and passes on the knowledge that those trees were the source of the plague that had harmed them in the first place, just as Noland and his crew are leaving the island, the entire village has this reaction.
In the Fishman Island arc, Jinbe 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.
A comedic example in the Zou arc, Usopp upgrades Nami's Clima-Tact, but Nami gets a little carried away with it, invoking this from Usopp.
Nami: It's easy to hold and even easier to twirl! You're the best, Usopp! (Unleashes lightning bolts at nearby Minks)
Nearby Minks: WAAH! WATCH IT!
Usopp: What have I unleashed?
Oh, how shall we count the ways in which Pandora Hearts does this to us?
Alice herself in Retrace 76 where she screams a big no upon seeing her sister die and say it's all her fault that everything happened. Then it turns into a Crowning Moment of Awesome when she decides to undo everything and wipe her memories.
In the Pokémon: The Movie Black/White movie, Damon realizes his mistake and falls into despair when both Reshiram and Zekrom, regardless of whether it was the Black version or the White version, show him that his decision to move the Sword of the Vale resulted in the dragon force going out of control. This shortly leads the misguided antagonist to pull off a Heel–Face Turn.
Alain upon being shown that his attempts to protect Mairin and Chespie by joining forces with Team Flare have potentially doomed the entire world. Thankfully, Ash snaps him out of it and the Kalos League finalists team up against Lysandre.
Sayaka 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.
Hardner from Rave Master has this when he finds out that Nagisa, the girl whom he tortured is actually his daughter.
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.
In Shokugeki no SomaIn Chapter 151 after Soma casually confesses to Erina's father and unknowingly to Erina and the rest of his dorm, of Jouichirou Yukihira being his father, Erina has a major freak out when she remembers all the times she has unknowingly insulted, her idol, his son, the cooking style, roots and the restaurant of said idol.
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.
Ellen in Suite Pretty Cure ♪ suffers this first hand as she watches a boy she had accidentally convinced to continue run away and his father be struck with a Negatone's wail, pushing them into despair. Bassdrum points out that she had done this so many times and, driven to despair herself, tosses away her Cure Module. However, Hummy's there to get her to realize that, deep down, she wants to make up for those times and helps restore her Heroic Resolve.
Sword Art Online: Asuna's father gets such a moment upon the reveal that Nobuyuki Sugou, for whom he had set up an Arranged Marriage with Asuna and genuinely believed to be a friendly, bright guy who he wanted to inherit RECT Inc., was in fact a major Bitch in Sheep's Clothing who not only conducted inhumane experiments on 300 SAO survivors, but also molested Asuna and tried to rape her right in front of her actual Love Interest Kirito; not only that, but when Sugou's crimes are made public, it causes a massive public scandal that not only causes the RECT Progress branch to collapse from lawsuits, but also impacts the main company itself. Asuna's father was so horrified at how badly he misjudged Sugou that he stepped down from his position as CEO of RECT, and Asuna herself just barely managed to convince him not to retire completely.
In the second Tenchi Muyo! movie, Ryoko's been incredibly suspicious of Mayuka, though the others are just blowing it off as Ryoko being jealous. Near the end of the movie's second act, Ryoko gets fed up and begins fighting with Mayuka and Tenchi gets between the two. Ryoko's begging Tenchi to listen before he lets his emotions get the better of him and slaps her. Tenchi's utterly shocked at what he's done, but is unable to apologize before Ryoko teleports away. It ends up being Ayeka who is able to get to Ryoko... just in time to prove that Ryoko's warnings were right.
In the final episode of I'm Gonna Be an Angel!, 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.
Tony in Toward the Terra after he accidentally kills Matsuka, a fellow Mu, while attempting to assassinate the antagonist. Complete with enough angst to last the rest of the series.
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.
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.
Windaria Izu/Alan when he realizes the magnitude of what he's done by flooding Itha/Lunaria and how many lives he destroyed.