Uncanny X-Men #150 gives Magneto a moment of this when he nearly kills Kitty Pryde in anger; he realizes he's become just like the Nazis that killed his family, and — for a span of almost a decade's worth of issues, at least—reconsiders his villainous career.
In Astonishing X-Men, the team is attacked by one of the giant Sentinels that murdered the population of Genosha. Kitty defeats it by kicking it up to full sentience. Suddenly capable of comprehending what mass murder is, with a machine's ability to actually evaluate all those deaths individually rather than just as a vague statistic, it suffers a Villainous BSOD and flies away in horrified remorse.
In his origin in Amazing Fantasy #15, Spider-Man has a classic one - Tears of Remorse and all - when he recognizes the burglar who murdered his uncle as the criminal he allowed to escape a page earlier.
In Ultimate Spider-Man, Norman Osborn accidentally kills his son while in his crazy goblin form. When he changes back he has one of these and asks a nearby SHIELD Agent to kill him.
JLA #15, the final issue of "Rock of Ages": In a Crowning Moment Of Awesome, in order to stop The Joker, who has the title reality-warping artifact, from wreaking colossal global havoc, the Martian Manhunter uses his telepathic powers to make the Joker temporarily sane. The Joker says "What have I been doing with my life?... I've been insane... Oh my god. What have I done?" It doesn't last.
The Old Man Logan storyline in the Wolverine comic is set in an alternate Marvel future in which the villains teamed up and successfully annihilated nearly all the superheroes. In a flashback, we see how the X-Men were done in: Wolverine and Jubilee are doing monitor duty when dozens of supervillains break in, intent on killing everybody. Wolverine meets all of them with deadly force in the inimitable Wolverine style. Just after he offs the last one — Bullseye — he turns into a dying Jubilee. Mysterio had set up an illusion, and Wolverine has just murdered all the X-Men, along with the mutant schoolchildren and staff.
This is Magog's reaction in Kingdom Come after he accidentally causes the destruction of Kansas.
It's Science With Dr Radium contained an "Ask Dr Radium" section on the fan mail page. One reader wrote in, asking "My God, What have I done?" Dr. Radium replied, "Um, you haven't given me much to go on. All I can tell you is that I've alerted the authorities, and hopefully they'll arrive soon."
Main character Matty Roth has this reaction in DMZ when he orders his private security force to chase and kill a group of soldiers who just gave him a crippling beatdown, (despite pleas not to do this) and he hears that his security people killed a group of Innocent Bystanders instead.
In Runaways, though in a very light manner: after Chase nearly gets Killed Off for Real because of drowning, when the team storms the Marine Vivarium, and Molly and Karolina argue about which way was correct to resurrect him. Fortunately, Gert followed Molly's advice, leaving Karolina pondering about what she nearly caused. Though that lasts about 2 seconds (Angst? What Angst? ?).
During Final Crisis, when Superman and Mandrakk have their first battle, Zillo Valla tries to give Supes advice from the sidelines. Mandrakk kills her to shut her up, then realizes in horror who she was: his former lover. However, after a second of grief, he blames Superman for his mistake and keeps attacking.
Prickly City: Electing Kevin, the Lost Bunny of the Apocalypse, to the Senate.
GOOD LORD, WHAT HAVE WE DONE?
In the first issue of Crystar Crystal Warrior. when Moltar has been manipulated into stabbing his brother Crystar and (wrongly) believes he has killed him, he cries "WHAT HAVE I DONE?" A few scenes later, when his actions lead to him and his followers being turned into monsters (as they will remain for the rest of the series), he has a single Beat Panel of blank horror as it all sinks in... and then composes himself and loudly embraces this fate, for the benefit of his followers if nothing else. Moltar remains a rather reluctant Big Bad through the whole series' run, deeply unhappy about what his actions have made him.
In Invincible, the titular character reacts this way after accepting An Offer You Can't Refuse, even though it was the only way to avoid an Earth-Shattering Kaboom. So when he says the trope's title out loud, the character making the offer responds "You have saved the lives of every living thing on this planet".
Invincible loves this trope. Another issue had Invincible go into a rage and quite literally beat Angstrom Levy into meat, before realizing he's not invulnerable like himself. "I thought you were stronger..."
This is actually Ghost Rider's schtick with the Penance Stare, forcing those to confront all of their sins. The best use of this was in the 1995 Fantastic Four cartoon, where he takes down Galactus.
In one Diabolik story inspector Ginko has this reaction after he realizes why Eva Kant was kidnapping people with the same blood type as Diabolik: the King of Terror was suffering from radiation poisoning and needed a full blood transfusion, for which Eva needed as much blood as five or six persons had. To try and not kill anyone, Eva was kidnapping a lot of donors, but Ginko discovered and stopped her after the fifth kidnapping, and she immediately performed the transfusion by taking all the blood of the kidnapped donors.
Early in Superman's Post-Crisis career, he was forced to execute a trio of Kryptonian criminals, breaking his Thou Shalt Not Kill rule. He's so guilty of doing so that he ends up sleep-crime fighting as Gangbuster and doesn't realize this until an encounter with the Guardian has the hero shred Gangbuster's outfit and reveal the S-Shield underneath. When he does realize this, he's so shaken by it, he decides to exile himself from Earth and stays that way until he finally comes to grips by it.
Spider-Man's been doing this recently concerning Doctor Octopus. The first was during Ends of the Earth, when he realized that all of Doc Ock's equipment was made from his inventions. He does it again in Dying Wish when, stuck in Doc Ock's dying body, he orchestrates a break-out and nearly involves the Lizard in the attempt, making him realize that he's probably starting to act like the madman himself.
Doc Ock also has this after Peter forces him to relive Peter's memories.
Ulic has a massive one when he kills his brother. This knocks him back to the light side, but he also spends the next decade in self-imposed exile and looking for a place to die in isolation.
Morbius says this in Punisher v7 #12 when Hellsgaard and his men have entered Monster Metropolis and start killing the monsters indiscriminately. They are in search of the stone Morbius has in his possession; if he had given it up like the molten preacher suggested they would have been safe.
The trigger scent sends X-23 into a blind, murderous rage in which she will kill anyone marked with it, Friend or Foe, and no matter how much she cares about them. Because of this, she's been consistently shown to be very sensitive about its affects on her, and is deeply traumatized when Zander Rice uses it to force her to kill her sensei (after which Laura is shown to begin cutting herself with her claws) and mother. Most recently, the revelation by Stryker, Jr. that Arcade posted footage of Murderworld, particularly her trigger scent-fueled rages, to the internet sends her crashing hard into a Heroic BSOD upon learnin the whole world has seen her in that state.
In Batman, Incorporated, a distopian future is shown wherein Gotham is in flames and Joker venom has become a plague essentially, and the few survivors are holed up in Arkham Asylum. Batman (Damian Wayne) brings a child that does not show signs of the strain, and thus must contain the cure... but is actually a carrier, and Barbara realises this, killing the baby. She completely breaks down afterwards, telling Damian that the Joker succeeded in turning them into monsters, and opens the gates so the insane mobs may kill everyone inside Arkham.