More seriously in Identity, Chloe Sullivan's horrified expression after under the influence of Brainiac, she renders the bad guy of the week catatonic by overloading his brain with information to protect Clark.
Stiletto, when Chloe dumps the body of the gangster Doomsday killed when he attacked her. She does this a lot...
And in Sacrifice, Zod's reaction when he killed Faora. Along with her unborn child.
Also played for laughs in Friends: Chandler has his "nubbin" removed after a squicked-out date leaves him. He misses an obvious joke, then cites the nubbin as the source of his "powers." He then says "Oh dear God, what have I done?"
Cheers. Carla once asked Frasier: "When you and Lilith wake up in the morning, which one of you is the first to scream, 'My God, what have I done?!'"
In another episode, this is essentially Fraiser's reaction upon fully realizing that he has successfully launched Woody Boyd's political career. (Cue visions of atomic fireballs.)
In Season One, Diane goes through a non-verbal version of this, after Coach and the others convince her to throw a baseball down the hall into the pool room, where Coach is standing. It Makes Sense in Context—Coach is proving a point to her about his uncanny success at bunting...with his noggin. It's even worse for poor Diane when you consider that she fully expected to miss—but as Sam notes, that's part of the point.
Faith does this twice. First when she accidentally kills Alan Finch, screaming repeatedly "I didn't know!", and when she remembers what she did to Wesley and Buffy.
This is also plainly evident in Willow's expression in "Once More With Feeling" when Buffy lets the Scoobies know that when they brought her back to life they pulled her out of Heaven.
Spike after the Attempted Rape in "Seeing Red". In a rather disturbing take on the trope, he seemed almost as distressed about his inability to go through with the act as he was by the fact he attempted it at all.
Spike: "What have I done? ... Why didn't I do it?"
Angel after the gypsy curse personifies this trope. He now believes he has to atone for what he has done.
Buffy has this twice, once in Season 6, when she learns that she didn't come back wrong and has been doing all sorts of horrible stuff of her own free will, and again in Season 8 when Giles is killed, magic is destroyed, and the Slayer line is ended, as a result of her space frak with Angel.
Angel, after he turned good again from being evil having tried to kill Buffy multiple times, murdered Giles' girlfriend, and ALMOST banished the entire population of Earth to hell he was so wracked with guilt that it eventually caused the decision to leave Sunnydale forever, which in turn began his own spin-off series.
On the Angel end is Gunn's epic version of this after his part in Fred's death.'
And Wes's equally epic one after he went literally Ax-Crazy in "Billy". He was under a spell, but it didn't matter, he still hated himself.
Wes also had one after he shot what he thought was his father in "Lineage".
On The A-Team: Face's expression after he pushes Murdock to the ground during their fight in Family Reunion borders on this. It's kind of a combination "What did I just do?" and confusion over the fact that Murdock doesn't seem the least bit angry with him for doing it.
Arrested Development uses a variation of this, "I've made a huge mistake". The phrase is used for comedic value, though. It was first said by GOB in "Key Decisions", and used by various characters afterwards, although it does remain primarily GOB's catchphrase, as he uses it at some point in most episodes.
Londo has several moments of serious regret as his schemes to restore Centauri power and glory play out... though that doesn't prevent him from going through with them until matters reach the point where Centauri Prime itself is at risk of annihilation.
The most heartbreaking instance may be when G'kar, his longtime nemesis, accepts an official apology from the Centauri Emperor for crimes committed against the Narns and approaches Londo in good spirits, extending a tentative hand of friendship. The problem: Londo made a deal with the Shadows only hours before that would result in another Narn-Centauri war. The look on Londo's face as he realizes his mistake is Tear Jerking.
Londo gets a lot of these moments. In the same episode, when the Centauri Emperor is on his deathbed, Londo tells him how the Centauri have attacked a Narn colony, kicking off a terrible war to further the Centauri's expansionist ambitions. The dying Emperor whispers his last words to Londo. Londo tells the other Centauri present that the Emperor told him that he would want them to continue, and to "carry my people back to the stars". But what did he really say?
Londo: He said... That we are both damned.
Another instance of this happening to Londo (Seeing a pattern?) made it into latter season's credits, with Londo watching the orbital bombardment of the Narn Homeworld with outlawed Mass DriversSee Here. (spoilers, obviously)
Also in that show is Delenn upon watching Dukhat die after being attacked by Earth Alliance warships orders their immediate destruction. "NO MERCY!" When she calmed down she was horrified to learn that her actions had started a full-scale war.
In the second season finale, Captain Sheridan gets one after he orders the station's defense grid to open fire on a Centauri cruiser in self-defense, resulting in the cruiser's swift destruction. Definitely justified, in that every action he had taken had been with the intent of protecting lives, rather than taking them, only for him to be backed up against the wall and only left with the one option. He has a similar reaction midway through the third season when he does the same thing... to an Earth Alliance destroyer.
iCarly: Freddie utters this line as a group (What have WE done?) when the gang realized that bringing back Marta made Lewbert's life even worse.
Carly went into a breakdown of repentance in iChristmas when her wish turned her life into one she did not want.
Freddie again evokes a variation of this trope in the extended version of iSaved Your Life. After his break-up with Carly, his face changes expression while in the elevator and asks himself in regret, "What did I do?" Cue a zoom out of the Bushwell building as Freddie yells "WHAT DID I DO?!"
The Carpenter has one in the SyFy miniseries Alice, right after breaking through his memory block and remembering his past life as Alice's father, then realizing it's a problem that he's spent the last ten years of his life sucking emotion juice out of people. Redemption Equals Death
A 'My God, what have YOU done' moment happens at the end of the Peacekeeper Wars in Farscape. For four years people have been chasing John Crichton, killing, raping and attacking him and his friends for his wormhole knowledge, and he finally gives in and builds the thing to protect his wife and newborn child, and it turns out that wormhole weapons he's been telling everyone are horrific, galaxy destroying weapons that no one should ever have under any circumstances are actually just as bad as he always said they were. When he turns it on, even those most desperate to have them realise just how bad it is.
(The wormhole weapon has been fired, and threatens to consume the entire universe.) Crichton: Here's how it lays out. Are you listening Stahleek? Grayza? Wormhole weapons do not make peace. Wormhole weapons do not even make war. They make total destruction, annihilation, Armageddon. People make peace." Chiana: Crichton, can you stop it? Crichton: I don't know, Pip. Maybe it eats the whole galaxy, a monumental black hole, a giant whirling headstone marking the spot where we all used to live and play and slaughter the innocent. Scorpius: (softly) This is insane, Crichton. (John lets out a choked laugh.) Crichton: God! Four years on and you're finally getting that!
A far more literal example is when Crichton has been forced to kill Aeryn while possessed by the Neural Clone. In this case, Crichton really does say "My God, what have I done?"
Jerry Seinfeld, after he gets engaged to Jeanie Steinem, a woman exactly like him...
I think I may have made a big mistake! All of the sudden I realized what the problem is! I can't be with someone like me! I hate myself!
In Battlestar Galactica, Gaeta, during the mutiny on Galactica in season 4. After Gaeta helps Zarek take over Galactica, Gaeta insists on giving Admiral Adama a court-martial for conspiring with the Rebel Cylons. But when Zarek has the Quorum of Twelve gunned down for refusing to recognize him as President over Laura Roslin, Gaeta has a bit of a revelation while looking over their dead bodies.
Sharon (Boomer) has a change of heart when she sees the experiments being done on Athena's daughter.
Baltar learns that he gave the Cylons information that helped them to kill billions of people.
The originalMy God, What Have I Done? moment, when Boomer finally 'regains consciousness' and sees the aftermath of her actions in the Season 1 finale. And the thematic continuation, the Season 4 premiere has Tigh experience a sort of 'waking nightmare' where he imagines the consequences of not owning up to the horrible truth of what he believes himself to be — killing Adama — and is horrified by the thought.
The Ninth Doctor had one of these in "The Parting of the Ways", when he forcibly sends Rose back to her own time in the TARDIS to protect her from the Daleks, only for her to absorb the power of the Time Vortex itself to get back and save him. He is truly distraught as it threatens to burn up her mind: "The power's gonna kill you, and it's my fault!" He sacrifices his Ninth life to save hers.
The Ninth Doctor also had one of these in the previous episode, Bad Wolf, where he looks down on a ruined Earth, populated by people who do nothing but watch horrific game shows and realises that it all happened due to his actions earlier in the series.
The Tenth Doctor had one in "The Waters of Mars". The Doctor saves people whose deaths will trigger the Golden Age of space exploration. He realises the impact of his interference when the key survivor realises what has happened and kills herself. The Doctor is subsequently horror-struck and has a massive Heel Realization.
The full force of this seems to finally hit him in "The End of Time";
The Eleventh Doctor had one in "The God Complex". A beast attacks his friends, and the Doctor thinks that it feeds on fear, so he tells them to focus on their faith. More people die much more rapidly after that, and Amy, his companion, is particularly affected. The Doctor realises that the monster doesn't feed on fear, but on faith. Since Amy basically sees him as a God, it's her adoration for him that will kill her. He breaks her faith with a Zero-Approval Gambit and unceremoniously drops her off at her house, planning to never speak to her again.
Amy Herself has one at the end of "The Impossible Astronaut", when she shoots someone in an astronaut suit who retracts its visor to reveal a little girl.
Chapelle: I'm like, you can't say skeet on the radio! You know what's so dope about skeet? White people don't know what it means yet. When they figure it out, they'll be like My God, what have we DONE?!
Kat from Power Rangers, when Rita's spell over her broke and she realized everything that she'd done to Kimberly.
In the first season Tommy has one immediately after Rita's spell is broken. It is probably justified because he should be going into shock.
Ransik says this in Power Rangers Time Force, when his obsession with revenge on all humans causes him to hurt his daughter, the only person in the world he loved. In fact, he loved her enough to end his quest for vengeance after harming her.
On Glee, when Sue goes into a deep depression, Will has a silent version of this, after a mild What the Hell, Hero? from Kurt.
In the 1998 Merlin series, Arthur has this reaction after Merlin calls him out for sleeping with Lady Marie, who was actually his half-sister. In the novelizations, this was taken up to full-blown Heroic BSOD that lasted for years.
In the Merlin series, Arthur goes into this trope after killing a captured rival king in "His Father's Son".
Later in the series Guinevere is given an enchanted bracelet that rekindles her feelings for Lancelot and leads her to make-out with him on the eve of her wedding to Arthur. They're caught, and the trope is played out in a truly heart-rending manner. Since Gwen never discovers that she was enchanted, she honestly has no idea why she betrayed Arthur - she didn't want to, and she can't understand why she did. The question: "what have I done?" is taken quite literally.
Michael from Prison Break wonders this for having (indirectly) lead to several deaths.
In an episode of Strong Medicine, a boy comes into the hospital after having a police officer use a Taser on him (They later find out that the only reason he reacted so badly was because of mercury poisoning.) Lu then spends the entire episode going into an Ideological Screed against the female cop. Later on, another boy comes into the ER, with the same cop. She mentioned that she was chasing him and reached for her Taser, but hesitated. Lu began to praise her (and herself) for this, but then the cop mentioned that, because she hesitated, the boy ran out into traffic and got hit by a car. It was especially notable because Lu was a textbook Jerk Sue and Canon Sue, so seeing her beliefs backfire was unique.
In LOST, Jack has this reaction after finally escaping from the island.
In "Amok Time", Spock, believing that he murdered Kirk, has this reaction so badly that he seemingly loses his will to live.
In an episode of Star Trek: Voyager, Torres utters this exact line when she realizes the race of robots she is helping were responsible for the extinction of their creators.
Another from Voyager was the Doctor realizing that he had disregarded his medical training and chosen to save his friend instead of someone he barely knew in a crisis situation. Being a medical program with a vast amount of ethical programming, he enters an almost literal Heroic BSOD over the matter.
To be clear: There was no difference between the two cases from a medical standpoint, but he could only save one and he had to make a snap decision; it wasn't that his ethical programming failed so much as that he had never been programmed in how to make a decision where there was no obvious logic to indicate a correct choice (or, in fact, an obvious correct and incorrect choice). He didn't actually do anything wrong, he had the reaction anyway because he couldn't figure out a medical way to justify his decision.
In The Closer, after several episodes of not feeling any remorse for facilitating a Vigilante Execution the previous season and not taking the victim's family's lawsuit against the department seriously, Brenda finally breaks down sobbing "What Have I Done?" at the end of season 7 episode 5, after everyone in her unit, plus Chief Pope, Commander Taylor, and her husband are all subpoenaed.
On the third-season finale of The Big Bang Theory, Howard and Raj make an account for Sheldon on an online dating site. Sheldon gets matched with Amy Farrah Fowler, who is almost exactly like him. Howard's reaction when he sees the two together: "Good God, what have we done?"
Forever Knight's Nick Knight has several of these over the course of the series, many in the flashbacks where he's struggling between needing to feed to survive and not wanting to kill.
Brass had one in the CSI episode "Genetic Disorder", after spending the entire ep assuming Doc's wife really had cheated on him.
In another episode, a husband and wife kill their baby after he starts showing symptoms of a degenerative disease that killed their first son. They find out after it's too late that he was simply sick because of the pesticide his mother used in the garden, and if she had stopped using it, he would have been perfectly healthy.
Duncan on Highlander after he killed Richie in a demon-induced haze. His distress is so extreme that he immediately asks Methos to kill him.
In Season 4 of Heroes, Samuel has this reaction after murdering his brother, Joseph. He may or may not quote this trope by name, as Robert Knepper's well-done emotional performance makes it unclear whether he's saying "What have I done", or if he's begging Joseph to "Hold on".
In the Charmed episode "We're Off to See the Wizard", Phoebe utters this almost verbatim after using pyrokinesis — an upper-level demonic power — on Cole's new personal assistant.
In M*A*S*H, Father Mulcahy once impulsively punched out an unruly patient who hit him first during triage, when any delays in the selection process can cost lives. While the rest of the staff agree he was entitled, Father Mulcahey was kicking himself for some time afterward.
Hawkeye has this in the episode "Fallen Idol." He sends Radar to Seoul to "sow a few wild oats", and Radar subsequently gets wounded by enemy fire en route.
In the episode "O.R.", Frank Burns complains out loud about the difficulty he's having removing a wounded GI's kidney. On a hunch, Trapper goes over to look at the patient's X-ray... and shows Frank that the guy only has one kidney. While Frank's borderline incompetence in surgery is usually Played for Laughs on the show, in this instance he's shown to be genuinely shaken at the realization that he could have killed the man through his carelessness.
In Game of Thrones, Theon Greyjoy silently has this reaction after looking back at everything he has done, taking Winterfell, killing two orphan boys, then passing off their burnt corpses as those of Bran and Rickon. All because he wanted his fathers approval, but for him he already died in Kings Landing.
This is written all over Ser Loras Tyrell's' face as he sits near the corpse of King Renly Baratheon. He feels extremely guilty for convincing his lover to make a bid for the Iron Throne, as this path led to Renly becoming a target for assassination.
Shane Vendrell from The Shield gets a major one after killing Curtis Lemansky.
Jesse becomes depressive after shooting Gale. He also blames himself for the heroin overdose of his girlfriend.
After a deception allows Walter and Jesse to elude him, Hank is enraged to the point of severe Police Brutality against Jesse. After he calms down, he is visibly horrified at his actions.
After nearly five whole seasons of rationalizations and selfish justifications, Walter finally goes through an absolutely gut-wrenching one after kidnapping his baby daughter when he runs away from his wife and son after they turn on him. While he's taking care of her in a restroom, she says "Mama" and realizes, in that moment, that his actions over the course of the series have led to the destruction of his entire family, either through death or ruined lives. He tearfully has a phone conversation with Skyler where he acts like an abusive husband who threatened her to cooperate, in order to exonerate her to the police as well as to break ties with his family and leaves Holly at a fire station to be returned to Skyler.
Miss O'Brien from Downton Abbey is usually an unrepentant Jerkass, but when she deliberately places a bar of soap so that Cora will slip on it, hoping that Cora will miscarry and be forced to keep employing her, she looks at her reflection in the mirror while waiting for Cora to get out of the bath and says "Sarah O'Brien, this is not who you are." After Cora is injured and miscarries, it's even worse.
Each of the major character in Supernatural have this reaction at one point.
Sam after he finds out that by killing Lilith, he actually released Lucifer, and that him drinking demon blood didn't actually increase his powers- it was simply a Magic Feather that Ruby used to control him.
Dean after Alastair tells him that by breaking and accepting his offer in Hell, he opened the first seal that started the apocalypse.
Castiel after deceiving his friends, teaming up with Crowley, breaking Sam's mind, absorbing all the souls in purgatory and going on one hell of a power binge.
666 Park Avenue: Annie says this word for word when she realizes her way out of her deal with Gavin will lead to an innocent man's death.
NewsRadio: In the episode "Who's The Boss (Part 1)", there's a scene where Beth is trying to fix the coffee machine (due to Joe the Handyman being on strike) while Dave (who is known to be a coffee addict) nervously waits for it to be fixed so he can have his cup of coffee. Beth believes she finally found what's wrong, but she instead causes the machine to short circuit, making the problem even worse. In horror, Dave shouts to Beth "My GOD, woman, what have you DONE?!"
In one episode of the fifties run of Dragnet, the man who molested two four-year-old girls is horrified by what he's done.
In a Very Special Episode of Boy Meets World, Shawn has taken to drinking. His friends confront him and try to convince him to stop, citing his family history of alcoholism, but he rebuffs all their attempts until he shoves his girlfriend Angela into the door in anger. He is immediately appalled at this last action of his, even gasping "how did that just happen?" in horror afterwards, and it causes him to immediately stop drinking and seek help.
Even Jeremy Clarkson utters one of these in Top Gear. During the auction at which the trio bought their cars for the classic time-trial rally in Mallorca, he ends up overbidding for an Austin-Healey Sprite and only realises that he has to spend some of his own money on top of the initial budget after the auctioneer calls out his number and James tells him precisely how much he got the car for.
In the Get Some In! episode "Medical", Drill Sergeant Nasty Corporal Marsh tells the aircraftmen under his instruction that they could all be dismissed from their two years' National Service if one of them commits suicide. When AC2 Leckie comes in from being punished for making a few mistakes during drilling (having thus missed the earlier conversation), he says he would shoot himself if he had any ammunition for his rifle. The other airmen are intrigued by this and almost seem to egg him on. However, later that evening, they find Leckie and his rifle have vanished, and soon Marsh appears demanding to know why a round of live ammunition is missing from the armoury. The aircraftmen are left reflecting with horror on their inaction and even encouragement toward Leckie's suicidal thoughts... until he returns from a visit to the armoury where he learned how to avoid the mistakes for which Marsh punished him, and explains that the missing round of ammunition was just an arithmetic mistake.
Stargate SG-1: Replicator!Carter seeks Carter's help to prevent a replicator army from invading Earth's galaxy, which has become immune to the Ancient disruptor. Carter trusts her because she believes no-one with her personality could ever work with Fifth. It's the only thing she's right about. Replicator!Carter's plan is to gain immunity to the disruptor, destroy Fifth, distribute her immunity to the replicator army she's now take control of and establish a foothold in Earth's galaxy. Carter's shocked reaction is 'What have I done?'.