A HUGE one happened in the episode "Before The Dawn" of Young Justice: Miss Martian, who lately has been VERY trigger happy with the Mind Rape button, attacks Aqualad and leaves him a drooling vegetable... only during the Mind Rape, she glances into his memories and realizes that Aqualad never betrayed the team, but was a deep cover mole for both Young Justice and the Justice League, and all the supposed bad stuff he did were actually diversionary tactics to earn The Light's trust. Cue Heroic BSOD.
In an episode of The Angry Beavers, Norbert delivers this line in a neutral, almost bored, tone.
One of the best known examples is in the Looney Tunes short, "What's Opera, Doc?" where Elmer Fudd, after spending the whole short exhorting in Wagnerian time that he would "Kill the Wabbit!", laments what he's done after he does it. (He also does this in some other shorts, but this was the most recognizable instance.)
This goes back to the very first Bugs short, " A Wild Hare", in which he shoots at Bugs and then Bugs plays dead, causing Elmer to break down in tears and call himself a murderer.
Parodied in Futurama, in one of the "Anthology of Interest" episodes, wherein Leela kills the professor by pushing him into a pit of man-eating anteaters:
Professor: Ohhh, you've killed me! You've killed me! Leela: Oh God, what have I done? Professor: I just told you; you've killed me!
Also played straight after framing Fry in destroying a bottle-ship in the episode "30% Iron Chef":
*Sad violin solo* Zoidberg: What have I DOOONE!!!
Although a few laughs are mined out of it; the punishment Fry has received for said destruction is negligible and Fry doesn't seem incredibly bothered by it, but Zoidberg reacts as Fry is being sent down for murder,
Happens again in the third installment "Bender's Game", where Leela sortof kills an Eldritch Abomination incarnation of Zoidberg under the belief he is an evil monster, only to learn he is not and swears off violence for a portion of the film.
Played with again in "Jurassic Bark", after Bender throws the fossilized dog into a lava pit:
Bender: Oh, what have I done?
Zoidberg: You didn't do anything, don't beat yourself up.
Yet again, in "Law and Oracle", when Fry discovers he will shoot Bender in the future, parodying Minority Report:
Dragon Booster: While it did not happen in the show due to cancellation, fans on the offical forum all agreed that they exlicity did not want Moordryd's obviously-going-to-happen Heel-Face Turn to include a situation where he said "What have I done" in any way shape or form. Since the series was Screwed by the Network, we'll never know, but he seemed to be shaping up to be able to do without it.
In the episode "Fatherklok" of Metalocalypse, Skwisgaar says this after pushing his stepfather in a fit of rage and causing him to hit a coffee table - it breaks underneath him, and he groans in agony as he looks at the shards of glass embedded in his hand.
Inability to admit her responsibility for anything that's happened to her is Demona's defining trait, and the only way she can deal with the endless guilt. The same thing is later said by John Canmore, one of the siblings from a long line of gargoyle hunters, which Demona also happened to be the source of, making it pretty ironic.
Xanatos himself has such a moment when he realizes in horror what he unleashed in creating Thailog from his Machiavellian smarts and Goliath's brawn.
And in the pilot, the wizard who originally cursed the Gargoyles to stone sleep when he thought that the princess was killed, but soon realizes his mistake after she turns up alive. Worse, because the page that contained the spell to undo the curse was burnt up.
Parodied in The Simpsons episode "Simpsons Tall Tales". In a retelling of the Johnny Appleseed story, Homer realizes he singlehandedly hunted the buffalo (their main food source) to extinction:
Homer: What have I done? What have I done???
Bart: Dad! Look! There's still two left!
[Whip Pan over to two buffaloes who are promptly shot dead]
Homer: (holding a still smoking shotgun): What have I done? What have I done???
Also parodied in "Homer's Odyssey", when he steals and breaks open Bart's piggy bank for beer money:
Homer: Oh no! What have I done? I smashed open my little boy's piggy bank, and for what? A few measly cents, not even enough to buy one beer. Wait a minute, lemme count and make sure... not even close.
Homer: What have I done?! What am I doing?! What will I do?!
Also in the episode "24 Minutes" Martin betrays the good guys by handing Bart over to the bullies in exchange for his Ant Farm. After realizing what he did and the consequences of it, he says "What have I done?!" out loud. Martin goes to a nearby room by himself as dark, sad music plays. We then see him hanging himself... until the camera pans out revelaing he's hanging from his underpants, thus giving himself a wedgie
Another example (although not word-for-word) is when Jimmy himself (accidentally) becomes a hall monitor in "Hall Monster". He goes... a little too far. Like, locking people in detention IN CAGES "to far".
In one episode of Pinky and the Brain, the Brain starts to realize that he has a problem when he goes a little crazy and accidentally pushes Pinky off of the table (or whatever it is that they're on):
Brain: What have I done? Pinky! Are you all right?
Pinky: Uh huh. Narf! But I'm afraid my secret playhouse will never be the same... (he had landed on top of it.)
Brain: Oh, it's all my fault. This obsession with taking over the world is causing me to hurt the ones I... tolerate.
This event prompts Brain to go to an organization called Megalomaniacs Anonymous in an attempt to get over his obsession with world domination. In a subversion, he decides in the end to return to his quest, since it's actually "a mission of mercy" — if he ruled the world, it would be a better place for everyone.
This ties in with a subdued, implied Mind Screw of the series: the title song only promised that "one is a genius, the other insane" but never stated which was which.
Played for laughs when Brain concocts a scheme to use a time machine to alter the past in order to make mice the dominant species, therefore making it easy for him to take over the world. He succeeds, but unfortunately, all the mice citizens are basically Pinky clones, horrifying Brain. He quickly tries to reset everything back to the way it was as he didn't even want to think about ruling a world of idiots.
Pinky: But why, Brain? With things like this, it should be easy for you to take over the world.
Brain: That may be true, Pinky, but who would want to!?"
Played without dialogue in the Christmas Special, after Brain ignores Pinky sobbing over his "stupid letter" to Santa he never got round to delivering, and eventually confiscates it in anger. Just before his plan is set in motion, he reads it out of curiosity, to find it is in fact a heartwrenching speech about his "best friend in the whole world, the Brain" and pleading for Santa to give every present intended for Pinky to him instead, since he never gets any reward for his hard effort. By the end of the letter, Brain is left in blubbering tears from remorse and aborts the scheme.
An episode of Batman: The Animated Series features a robot clone of Batman that seeks to kill Batman and take his place. Once he (apparently) succeeds at this, he goes through an existential crisis since the real Batman wouldn't kill anyone. He cries out "What have I done? I've taken a life!" and proceeds to smash the console evil supercomputer HARDAC was attempting to use in its evil ploy, both stopping the program and electrocuting himself, prompting the real Batman (who was hiding on a conveniently placed cliff crag) to wonder if his robot duplicate actually had a soul.
In Justice League Unlimited, when the League's Kill Sat not-all-so-accidentally fires upon Cadmus HQ, Superman rounds up the founding members and questions: "What have we done?" Doubly subverted, though: First, they tell him that they haven't done anything, since someone else hijacked their main computer. However, he replies that it was their choice to keep the orbital cannon, therefore all of them must take the responsibility.
Done earlier in Justice League in the episode "Hereafter" when Superman was shot into the future. He finds the last human alive, Vandal Savage, who recounts how he destroyed the entire solar system in his quest for power. When he prepares to send Superman back to his time to stop him, they have the following exchange.
In Space Ghost Coast to Coast, one episode deals with a pledge drive that's not going very well. Frustrated, Space Ghost orders the audience to give him money, or he'll shoot Brak. Brak starts crying, and Space Ghost feels ashamed of what he's doing. Brak calms down and tells him that "it's okay", which Space Ghost cheerfully takes as permission to shoot him.
In another episode, Space Ghost takes revenge on Zorak for thrashing his apartment by blasting him so many times he ceases to exist (or so he thinks). When he realizes that he actually killed him, Space Ghost shouts "Heaven help me, what have I done?!" before casually following up with "Oh well" and continuing the show without him.
In a third episode, Space Ghost's pet sea monkey Banjo grows to immense size and starts blasting Zorak, causing Space Ghost to bellow "What have I unleashed?!" Then Space Ghost kills Banjo, which prompts another moment.
Zuko had an extended one for the first half of the third season. His hasty actions at Ba Sing Se started to seem less heroic and more despicable, culminating in his goodbye speech to Ozai during the invasion.
Sokka doesn't say this out loud, but after seeing him relive the memory of his dad leaving after he kicks Aang out of the group for hiding his father's map, his face tells he's thinking of something like that.
Right after yelling at Aang in the episode The Waterbending Scroll, Katara immediately feels ashamed for doing so. The look Sokka gives her plainly says "What the heck is wrong with you?!"
Aang's reaction to burning Katara in The Deserter.
This was Sozin's reaction to starting the war during the twilight of his life. He asks himself Was It Really Worth It?, and concludes that no, it wasn't.
Played for laughs in Sequel SeriesThe Legend of Korra, when Tenzin helps his son Meelo train his lemur Pokey...only for Meelo to have soon trained LOTS of lemurs! Tenzin merely mutters "I've created a monster".
Suyin's reaction when her attempt to avoid arrest ends up scarring her sister Lin.
In "Sisterhooves Social", Rarity totally loses it with her sister after an entire day of getting on one another's nerves (including when Sweetie Belle makes a picture out of the rare gems Rarity had been saving for a dress for an important client), resulting in a huge argument which makes both swear that they wished they were only children and storming off. Later on she's tidying up and looks at the picture again, shown for the first time to be a picture of the two nuzzling inside a shining blue heart. Rarity’s reaction is almost word for word.
She sings "what have I done" in "Rarity Takes Manehattan," when her friends don't show up for her fashion show and she thinks she has alienated them. They actually just overslept because they were exhausted from helping her sew new dresses the night before.
"Secret of My Excess": Spike doesn't come right out and say it, but the emotion is conveyed by his reaction to seeing Ponyville devastated, and his own giant footprints.
Happens in "Hearth's Warming Eve" when Clover the Clever (Twilight), Smart Cookie (Applejack), and Private Pansy (Fluttershy) discover that the blizzard that destroyed their homeland and is now threatening Equestria is caused by Windigos, winter spirits that have been feeding off ofthe hatred between the three tribes of ponies, meaning their pointless hatred for one another was the cause of everything that has happened.
In "Baby Cakes", despite being only a month old, the Cake Twins are smart enough to realize they've gone too far when they see Pinkie bawling.
The entire town of Ponyville gets one in "The Super Speedy Cider Squeezy 6000", when their support of the Flim Flam brothers almost causes the Apple family to lose their entire livelihood.
Fluttershy gets one in "Putting Your Hoof Down" after being a huge bitch to Pinkie Pie and Rarity, due to taking her assertiveness lessons from Iron Will.
Twilight has one in "A Canterlot Wedding" when everyone calls her out on calling Cadance evil. The twist is that it wasn't really Cadance at all, but an imposter posing as her.
Thus, when she reveals that the first Cadance she met is an impostor by helping the real Cadance escape, everyone else has this when they realize she was right. The impostor, the changeling queen Chrysalis, rubs into their faces that if they had just listened to Twilight, she could have been stopped. Applejack goes to apologize to Twilight during the Near Villain Victory, but the latter brushes it off and doesn't hold against them, stating that Chrysalis had fooled everypony and that it wasn't their fault.
The Cutie Mark Crusaders, fed up with Babs Seed bullying them to impress resident bitches Diamond Tiara and Silver Spoon, set her up for a humiliating fall. Then they learn from Applejack that she's being bullied herself back in Manehattan.
All three: WHAT'VE WE DONE!?
Discord of all people has one of these moments in his returning episode when he realizes that Fluttershy, the only pony to have shown faith and trust in his rehabilitation, takes his jokes and her patience too far when he floods Apple Acres.
Twilight says "What have I done?" in "Magical Mystery Cure" after discovering that her careless use of magic has ruined her friends' lives and made all of Ponyville miserable, and she doesn't know how to undo it..
In Twilight's Kingdom Part 2, Discord is obviously having second thoughts during his team up with Tirek. But this trope doesn't hit him completely until Tirek, unsurprisingly, betrays him and takes his power, just like he did to Fluttershy.
A comedic version happens in Animaniacs short "Temporary Insanity", twice to Mr. Plotz. The first time is when he realizes that instead of calling a temp agency, he's called the Warners and told them he needs help in the office while his secretary is out sick. The second time is when he ''agrees' to the Warners helping him out. Needless to say, his fears do not go unwarranted.
In an episode of the Krazy Kat animated series, Krazy is Born Lucky, and Ignatz is jealous and wants her luck for himself. Then he comes up with the perfect solution—he'll give her some Cement Shoes, get her to sign her luck away to him, then dump her underwater. Only after he's already done this does he have this reaction and dive underwater to save her.
During a Halloween episode of Hey Arnold!, the kids go trick-or-treating disguised as aliens. Unfortunately, a The War of the Worlds-style radio broadcast convinces the adults that it's an actual alien invasion, who then form a lynch mob out to get the kids. (It doesn't help that they accidentally used exterior latex paint instead of facepaint, which doesn't rub off.) At the climax, Bob Pataki grabs Helga by the neck and starts choking her, only to realize his mistake when it starts raining and the paint finally washes away.
"I almost killed my own daughter. I'm a monster!"
Arnold felt this when he blinds Helga on April Fool's Day.
Rocket says this almost word for word in the season 2 episode "The Fallen Star", after realising his Netherball opponent is actually Tia.( he thought he was playing against various previous opponents)
In episode 2 of The Legend of Prince Valiant, Valiant stumbles into the territory of a large man who angrily orders him to get out and attacks him. Valiant defends himself, but loses his temper and nearly beats the man to death. While Arn says he was justified, Valiant is horrified and atones by treating the man's injuries and taking him to his mother.
In the first season finale of Dragons: Riders of Berk, Mildew has one when Alvin decides that he's outlived his usefulness, throws him in prison with Hiccup, and prepares to serve him his pet sheep as his last meal. Turns out to be a subversion as it was part of a Xanatos Gambit so Mildew could learn Hiccup's knowledge on dragon taming to teach Alvin and his men.
Jackie Chan from Jackie Chan Adventures yells this in the second episode of season 3 when he realizes that destroying the talismans which results in its powers to be transferred to the animals is not really a good idea.
Captain Capacitor from ReBoot says this in a direct reference to Star Trek III: The Search for Spock while watching his ship, the Saucy Mare, get shot out of the sky onto enemy forces while packed with explosives.
While not uttered, Rabbit from The New Adventures of Winnie the Pooh has one of these moments after realizing Pooh was trying to help him in fetching honey (Before this, he had tricked Pooh into thinking he's moving away due to Pooh's constant borrowing for honey.) what follows is one of the show's more heartwarming moments.
In Dexter's Laboratory's "Way Of The Dee Dee," Dee Dee tries to make Dexter behave more like her, but she realises she's gone too far when he gets into it and begins smashing up his laboratory; she begs him to stop (which he does), wails "WHAT HAVE I DONE?!" and runs off sobbing. Dexter solemnly begins to repair the damage... and the cartoon ends.