8-Bit Theater is the perfect example of this. The main heroes are constantly called out for their atrocious behaviour, which they don't even try to hide. They are thieves, mass murderers, and mob bosses, among many other things.
Inverted in Looking for Group; Richard (a card-carrying 'joyfully and creatively Chaotic Evil' character' with centuries of continuous evil) get a 'what the hell antihero' reaction from hell because by killing/burning an entire village he ACCIDENTALLY did some potential good to the future of the region. This is the only part where we see Richard having a conscience (only he's guilty of doing GOOD)
Played straight with Cale calling out Pella for forcing the Gnomes to join Kethenecia by destroying their last line of defense. To be fair, after talking about the incident with Benny, he seems to be more disappointed with her than angry.
Also played straight recently, with Cale grabbing Maikos and using him as a human shield when being shot at by an archer... TWICE. In his defense, Maikos and the other people from his village have been established as undead and therefore both incapable of dying and practically immune to pain; the reason it's a What the Hell, Hero? moment is because Maikos told Cale that his people were becoming mortal again just before this event came up.
Doc also beats himself up emotionally in private, particularly when the ninjas he killed rise from the dead with no medical explanation and no obvious purpose except to get revenge on him. His guilt in the zombie ninja incident is assuaged, however, when it's hilariously subverted at the end of the story.
Gordito delivers a particularly thorough one here.
And follows it up when it seems the Doc still hasn't learned his lesson.
A Sluggy FreelanceStory Arc has Riff out to kill Aylee because he believes she's a threat to the world. Torg points out that, as a Mad Scientist whose inventions tend to backfire in catastrophic ways, Riff is actually more likely to wipe out the human race than any alien.
Torg often gives these to Aylee when she eats clients or other people, although they're more often treated as a bad habit than murder. When she, while still in a "Cannibals Anonymous" program, serves up a man for Thanksgiving Dinner and Zoe gets upset, he fires Aylee (but hires her back some time later after she reforms as a result of the program).
The reason why Torg treats this incident more severe than the others is that she killed the man just for a sick joke, rather than for feeding as usual. And she sought out the victim specifically for being an animal-loving philanthropist.
And now the Fate Spiders are getting one from Father Time, as their attempt to undo the Great Tangle actually made it worse.
Bun Bun and Gwynn frequently get called out for some of their stunts. This works as well as a chocolate kettle where Bun Bun is concerned. Gwynn, however, seems contrite after most but it never seems to stick. Neither are actual villains (tho this depends on your point of view when dealing with Bun Bun. Not sure Santa would agree) but I'm not sure you could call either of them technically heroes either.
In Tower of God, almost everybody calls out Koon for not supporting his best friend Baam any longer when he finds out that Baam is an Irregular. Out of protest, many who were unsure about supporting him now sided with Baam because they did not want to be like Koon. Who WANTED this to happen.
In Jack, the titular character leads a genocidal campaign against the human race. He NEVER stops getting chewed out for it, even though he's really a nice guy who, thanks to the power of Hell, can't even remember what he did. It's played straight once Farrago reveals that Fnar's stay and eventual molestation in Hell was her fault and Jack gets angry and attacks her, although he becomes intensely regretful and begs for forgiveness a second later. They haven't forgiven him yet.
In The Order of the Stick, Vaarsuvius the mage has crisped the evil noble who had been plaguing the party, just because it was more convenient than enduring another trial. To make things worse, V had no idea who the person killed was or what, if anything, he'd done to merit execution. Disintegrating Kubota was based solely on the time-consuming nature of a trial and the fact that Elan had tied him up. Elan, normally a Spoony Bard, calls V on it in a manner that shows his growth as a character.
And recently Vaarsuvius has been on the receiving end of an another lecture about making a Deal with the Devil. Whilst V's stated intentions are that the Deal allowed access to further ability both to save loved ones in danger and to continue the quest to help save the world, both laudable goals, Vaarsuvius' mate challenged that it was more about V's ego, the need to solve the problem alone and V's ultimate desire to taste ultimate power — a not entirely unreasonable charge, in light of the fact that V agreed to make the deal after being presented with an alternative that might have worked. Although it would not have worked, given later information that Durkon and Elan had left the fleet a few days earlier, Vaarsuvius was far too addled to weigh the actual chances of the plan, and simply focused on how it would have required the personal humiliation of requesting the help of others.
Although Vaarsuvius is already technically asking for the help of others by making the deal anyways.
It should be mentioned that the demons also pointed out the alternative plan had next to no chance of preventing the Ancient Black Dragon from killing the children, just from binding their souls and escaping. It wasn't just a matter of ego, V was also so obsessed with not failing again that s/he was willing to do anything to succeed this time.
Earlier, during Roy's initiation into the Lawful Good afterlife, he gets chewed out for abandoning Elan to bandits (he came around) and tolerating the obscenely evil antics of Belkar. Roy does defend himself, however, freely acknowledging that he was wrong to do the former and to his credit realized it, and that in doing the latter he has managed to prevent Belkar from doing even worse things than he currently does under Roy's guidance.
In another part of the story, Redcloak believes he is giving one to O-Chul for choosing to sacrifice several innocent lives just to keep a secret. Specifically, Redcloak is threatening to push them off a tower and into the reality tear if O-Chul won't reveal the secret of the gates (which he doesn't actually know, but Redcloak refuses believe that). Redcloak gets so indignant over how callous the paladin is about innocent lives that he seems to forget he's the one threatening them. In the end, he lets the prisoners live, certain that seeing how little O-Chul cares about them will ruin their morale, but it only strengthens them to see his resolve.
To put things into perspective, Redcloak had used every spell and tactic to find out the secret he thought O-Chul knew, but it all resulted in proof that O-Chul didn't know what Redcloak wanted (He really didn't). Redcloak states that this can't be logical, and so tells O-Chul that he must have some secret ability that prevents certain information from being discovered. And the entire time Redcloak is dangling the prisoners, O-Chul says he would gladly tell Redcloak what he wants to know if he knew it, but can't because he doesn't.
Redcloak later admits that he is now convinced O-Chul does not know anything.
A recent strip subverts it beautifully, with Lawful Good Roy deciding to use Chaotic EvilHeroic Comedic Sociopath Belkar as live bait to "guide" the giant sandworm they used as an impromptu transportation method. Belkar starts off Calling The Hero Out, then breaks into laughter, claims he almost managed to go through that with a straight face, and tells them to "dangle (him) away".
Miko Miyazaki gets so many of these that one might suspect that Rich Burlew has a serious bone to pick with characters (in RPGs or in real life) who twist the rules of law and good so far to meet their own desired ends that they appear evil to anyone else.
Similarly, when Annie explodes at Mort — over a misunderstanding of his intention in giving her a Blinker Stone — Kat actually says, "What the hell, Annie?"
Reynardine does it again when he catches Annie stealing Kat's workbook to copy her homework — again.
Jack Hyland ends up delivering one of these speeches to Annie in Faraway Morning, where Annie deliberately tries to hurt Jack — who had seemingly been sporting a crush on her — by rejecting him. This ploy, which fails because Jack has feelings for Zimmy, was apparently petty revenge for Jack's actions during Spring-Heeled Jack, when he was under control one of by Zimmy's spiders.
You did all this just to get back at me for something I didn't have any control over? You got some strange ideas about revenge, Carver.
In Angels 2200, when Whiskey reveals the final stage of her Break the Haughty plan to humiliate the newly promoted Quetz by poisoning her with laxatives, Loser responds by saying that she's gone too far. This proves to be true, as Quetz eventually finds out and has Whiskey arrested with the intention of having her court-martialed, even saying that she might have gotten off much more easily if not for the last prank.
In the last battle of the first part, Whiskey is called out in no uncertain terms for accidentally killing Loser.
Soon afterward, Bubblegum gets called out for having a Heroic BSOD and leaving combat after seeing Loser die and her blood on the cockpit window
Earlier on, Hammer (rightfully) dresses down Kid for not taking a clear shot on an enemy fighter that had a lock on Bubblegum. If Quetz hadn't made a near-impossible shot to take her down, Bubblegum probably would have died. This also marks a turning point in their relationship as a case in which Hammer is required to discipline Kid, thus raising the question of whether they can be friends (or perhaps somethingmore) as well as squad leader and subordinate.
The Light Warriors in 8-Bit Theater. White Mage describes them as "insatiable flying deathmongers". The rest of the cast is inclined to agree,though White Mage did admit that she made up the flying part. Taken to new heights recently with the culmination of Sarda's plot against the light warriors. He has waited the entire lifetime of the universe and more just to exact revenge. Then again, to call the Light Warriors "heroes" according to the modern definition is to miss the point.
Finally paid off, now that the 'hero' who defeated Chaos is WHITE MAGE and some others. Oh, and she had the villains be called the Light Warriors. The villains of the game are more heroic than them!
Towards the end of book 1, Parson subtlety called out Maggie for indirectly causing the death of Misty. He then acknowledges that since he just defeated the enemy in a particulary horrific manner, he's not one to talk.
During the book 2 text updates, Jillian makes it clear that she intends to try to turn the decrypted Ansom to her side. For his part, he's disgusted by her hypocrisy and cruelty in treating every decrypted but himself as some kind of monster and executing them without reasons.
Ansom: "We are alive." Jillian: (relieved) "I want to believe that." Ansom: "I know. But understand this: we do have a will. I choose to serve her, because it is through her that I serve the Titans. So if you think you can convince me to choose otherwise, then try! By all means, try to turn me. But what I have seen so far from you is not a very fine start."
In General Protection Fault, the cast is not very pleased with Fred's using his newfound control ability to possess Trent and force him to sexually harass Sharon, strip naked and run around calling himself Wiley Wombat, which caused him to get arrested.
When Fooker returns, Dexter complains about him tampering with his memories to replace his feelings for Sharon (who had recently broken up with Dexter, and who was rekindling her relationship with Fooker) with Megan Morrone so that Dexter could not get together with her while Fooker was working with the UGA. Fooker admits the move was selfish, but notes that Sharon wouldn't necessarily have taken Dexter back if he hadn't done it, with which Dexter reluctantly agrees.
Dexter later gets one for taking the Scott and Patty into "Bog Of Bloodbath", via the Mutex without Nick's permission, trapping them in there for days and almost getting fired for absenteeism. Patty is especially harsh on him for that, and is not willing to forgive him.
Meighan and Alisin do it to each other in a Fans!! story, in which they argue about an earlier occasion when the latter seduced the former to try and provoke a Break His Heart to Save Him situation with Rikk when she was dying (which didn't work, but caused no degree of tension following that). Meighan points out, not without merit, that Alisin has no place to hold a grudge since she was the one who did the seducing and Meighan was the one being manipulated. Alisin, equally with merit, points out that she was quite visibly in a bad place at the time and not thinking clearly, what with the whole "impending death" thing, and that Meighan should have resisted more than she did. The two eventually accept that the other has a valid point and bury the hatchet.
The Apple of Discord had a moment of this recently where Steve (who was in a coma from 1993 to 2008) finds out that main character Arthur was the one who accidentally put him in the coma in the first place. Then he finds out that, in trying to fix the coma situation, Art's summoning spell backfired and is slowly causing reality to collapse.
Far Out There had Layla do this to Ichabod upon realizing she could have been killed because he wouldn't own up to a simple mistake.
In Kevin & Kell, it's revealed that Rudy never sent Kevin and Kell's marriage papers as a bill banning interspecies marriage is up for voting, which would also threaten their marriage. Rudy claims he was bitter about Kevin becoming alpha male, and didn’t think there would be any consequences, and Lindesfarne notes that now all interspecies marriages are at risk, with the potential slippery slope to eventually prevent him from marrying Fiona.
Stein of Frankie And Stein gets a good one here after creating his Frankenstein's Monster, Frankie, from the aforementioned reanimated dead. Concerning taking a random brain and stuffing it in some poor girl's body, without even asking!
In Homestuck, Vriska is called out by both John and Tavros when she decides to prototype Jade's sprite with Becquerel, turning Jack Noir into a Physical God and breaking most of the enemies in the kid's session. This being Vriska, of course, whether or not she counts as a "Hero" is debatable.
The thing with Vriska is that she believes that she is a hero. Sure, she'll admit that she's also having her fun and that her plans coming to fruition will establish her as the great and powerful, and perhaps most important, misunderstood saviour of Paradox Space, but in the end, she's positive that it will work out for the greater good. For that reason, she's unafraid of being judged as a villain for doing what it needs to be done.
After watching someone else do awful things ostensibly for the greater good, Vriska understands why everyone hated her antics and calls herself out.
Artie, the genius gerbil from Narbonic prizes himself of being the resident voice of conscience and moral anchor of his group of mad and generally evil and dangerous peers. However, towards the end, his creator, Helen Narbon snaps at him in middle of a sermon and makes him realise how through subtle and well-intended manipulation and interference, he's inadvertently been the architect of the main conflict of the story, "causing more evil than all of them put together."