In Batman: Year One, Commissioner Loeb starts out as a typical corrupt cop, nasty in his own way but not extraordinarily bad. His true crossing of the horizon is when he firebombs an apartment building to catch/kill Batman, callously dismissing Gordon's concerns about the derelicts living inside (at least one of whom was killed in the bombing).
While the Joker was always portrayed as a total psychopath, it is generally considered that he crossed the point of no return in 1988 when, within a few months, he crippled Barbara Gordon for life and beat Jason Todd to death with a crowbar. If that doesn't count, then he did it during the No Man's Land arc, luring Sarah Gordon out with a bunch of kidnapped babies and murdering her in cold blood. The act is so vile that even he takes no joy out of it, walking out with a frown on his face for the police to arrest him.
He's breaking out all the stops in Death of the Family, but one particular stand out point is giving the hyenas, that he and Harley raised, rabies. These are pets that he and Harley personally raised since they were babies! All this to spite Harley for not waiting and praying for his return (never mind that he didn't leave any indication that he was going to) and for getting together with Deadshot.
During the Knightfall saga following Batman's paralyzation by Bane, he was replaced by Jean Paul Valley, who would become better known as Azrael, while undergoing therapy to restore the use of his legs. Jean Paul was a far more brutal Batman, with no Thou Shalt Not Kill code and a serious case of brainwashing by a fanatical cult, and he finally crossed the line in Bruce's eyes (and those of Gordon, Nightwing and the others) when he chose to allow the Serial Killer Abattoir to die rather than interrogate him as to the whereabouts of his hostage; as Abattoir was the only one who knew where the hostage was, this led to the hostage being crushed to death. This act led to Bruce's decision to take back the mantle of the Bat from Jean Paul.
Basil Karlo, the first to take up the moniker of Clayface, shows he's a monster inside and out when he captures and tortures Poison Ivy during No Man's Land, depriving her of sunlight while forcing the children she was protecting to grow fresh fruit for him to sell.
Subverted poignantly in Bruce Wayne: Fugitive, with David Cain. David is generally an awful person, but probably his most heinous crime is his treatment of his own daughter, who he abused horrifically in order to turn her into the perfect killing machine. The subversion comes when despite this, Batman makes it clear to Cain that Cassandra is still willing to forgive him, and that it's not too late for him to fix things. Cain, however, is too broken at this point to try.
A particularly dark example is in Batman: Bloodstorm, the second part of the Batman Vampire trilogy; initially, Batman might have been resorting to bloodier tactics than usual, but he was restricting himself to killing vampires, until he broke the Joker's neck and drank his blood after the Joker killed Batman's ally, Selina Kyle. Even after that, some of his allies felt that he hadn't completely crossed a line considering who he killed, but his subsequent murder spree in the final part of the trilogy, Crimson Mist, confirmed that the Batman that Gordon and Alfred knew was gone forever.
In Batman, Inc., Talia al Ghul proves she's just as much a monster as her father when she allows her own son Damian to be brutally slain by his own clone. She does have the decency to shed a few tears afterwards... which she dismisses as a moment of weakness. Even this ante is upped when you realize how many times Ra's has forgiven Talia's much deeper and constant betrayals. In her current spoiled brat persona, she cannot give her son such forgiveness even once, for being somewhat like the man she fancied. Even Ra's notes, with some twisted fatherly pride, that she has at last become a monster.
Zsasz using kidnapped runaways and orphans for gladiator matches and dumping their bodies in the river. You know it's serious when the current Robin Damian Wayne — a character who, in his first appearance, decapitated two of Batman's rogues, assaulted Alfred, and tried to kill Tim Drake at least three or four times — is vomiting over what happened. And while he has mellowed out by that point, he's still pretty unflappable.
Robin: Year One has the Mad Hatter brainwashing several young girls to sell them to a pedophile dictator, one of which was Dick Grayson's classmate.
Huntress crosses at the end of Cry for Blood when she arranges the murder of her own father, unless it happened earlier. The first Question calls her damned for it, but she replies that she was damned a long time ago. In Huntress: Year One, it is revealed that she considers the moment she murdered Stephen Mandragora to be the moment she crossed, thinking, as she killed him, "This is worth going to Hell for."
Batman (Tom King) sees Bane and the Flashpoint version of Thomas Wayne cross it when they engineer a plan to break Batman that includes the former killing Alfred.
It's difficult to pinpoint the exact point when Eobard Thawne crossed the line, given that his appearances add more and more atrocities to the list thanks to his abuse of time travel. At first, his status as a one-off Evil Counterpart was dispelled by him murdering Barry's wife Iris for refusing him. In Flashpoint (DC Comics), he goes back in time to murder Barry's mother, allowing him to cross the line long before he met Iris. And then future comics revealed that he wiped his brother, his academic rival, and all the men his crush ever dated from existence before he terrified said crush into a catatonic state for rejecting him one time too many.
Blackest Night: The Flash had fans of Captain Boomerang the Younger wailing and gnashing their teeth. Owen's moral compass is shaky at best. Upon learning of his heritage, he joined the Rogues with minimal prompting and showed very little remorse or hesitation when it came to killing people in certain situations. Those situations being fights. After leaving the Rogues, his character was more developed as a screw up who's looking for a family, and whoever's giving him affection and approval (or at least a group to hang with) gets his loyalty. He's had ice cream nights with Supergirl for pity's sake, and has always been more or less shown to be a pretty okay guy, for an occasional assassin. So in the latest installment of the series, we learn that baby-Boomer was feeding criminals to his zombie-fied father to somehow bring him back to life. Okay, a little creepy, but it's not so ba—Oh, wait, no — he fed zombie Boomer innocent women and little kids too, apparently! Thus making a formerly endearing, kinda sweet character... so full of squick.
In Gotham City Sirens #20, Harley Quinn crosses the line. During her bid to kill the Joker in Arkham Asylum she murders an innocent guard via explosive in the face. Even worse, she acknowledges that the guard is an innocent man, but she is too full of rage to care, and the guard is too intelligent to be distracted by other means.
In Emerald Twilight, Hal Jordan crosses the horizon when he kills Kilowog. At first, Hal is just beating up other Green Lanterns and stealing their rings with the rational that they would have enough reserve energy left to make it to safety. Then Hal snaps Sinestro's neck, but Sinestro was always a monster. But when Hal atomizes Kilowog, who is the only person left standing between him and the central power battery, that's the moment. Even Hal admits that he crossed a line and doesn't deserve to wear the ring anymore.
Nekron of Blackest Night is an Eldritch Abomination who is said to be Above Good and Evil, and at first, he seemed like that. Raising the dead as foot soldiers and sending them to terrorize their loved ones? That's pretty ruthless, but not exactly personal. Turning all the resurrected heroes into Black Lanterns against their will? More evil, but considering that he's the literal embodiment of death, it's understandable. However, once it's revealed that the living heroes who are turned into Black Lanterns are conscious and forced to watch as their possessed body is used to attack their loved ones, all the while slowly wasting away until they turn into a Black Lantern for real, Nekron goes from force of nature to vile monster.
The Guardians cross the line in the early issues of Rise of the Third Army when they wipe out Ganthet's emotions to turn him into a cold emotionless Guardian like them. Kyle is understandably outraged by Ganthet's emotional lobotomy and vows to fight the Guardians.
In Identity Crisis (2004), the previously bumbling and mediocre villain Dr. Light is revealed to have raped the Elongated Man's wife, Sue Dibny, on the JLA Satellite years earlier. What he was doing there in the first place isn't revealed, nor was it the first time he'd done it. Unfortunately, that wasn't the worst thing that happened to Sue in the book.
Superboy-Prime is presented as a confused teenager with powers he can't control lashing out at people who don't understand him... until picks a fight with the Conner Kent Superboy and is jumped by the full Teen Titans roster. He loses control of his own strength when he fights back, killing some of them and provoking a My God, What Have I Done? moment. At that point the Flashes drag him into the Speed Force, where they imprison him for an unknown length of time. When next we see him, he's turned into a near-demonic Card-Carrying Villain, threatening to kill even his friends and allies to get what he wants and excusing his actions by claiming to be "better than those losers".
If he didn't cross it there, he certainly crossed it when he killed Earth-2 Superman. While the above is rather monstrous, at the very least Prime had gone through a lot of hardships and had been convinced by Alex Luthor, Jr. that they were in the wrong, not to mentioned he was still trying to get back Earth-Prime. Earth-2 Superman isn't one of the heroes who Prime thinks is "corrupted", but a survivor, friend and the original superhero. Superboy-Prime kills him nothing more than blind and callous fury at him stripping him of his powers.
In one of the Infinite Crisis lead-ups, Villains United, Alexander Luthor (under the guise of the regular Lex) orders part of his Secret Society of Villains to retrieve a number of people for unknown reasons, chief amongst them the heroes Lady Quark and Pariah (who fought alongside him during the original Crisis). Alex mocks and kills Pariah and later uses Lady Quark to power his dimensional tuning fork. Again, they were all heroes who tried to save the Multiverse together. In the actual Infinite Crisis, he just keeps on going with his despicable manipulations of everyone, including Golden Age Superman.
From The Sandman (1989), Doctor Destiny's Diner of Death. Justice League of America villain John Dee may have kicked the dog when he shot a woman who had been nice to him, but the real proof that he had turned irrevocably evil came next issue. Sure, he would routinely plot to drive the whole world insane back in the silver age, but what he does to those six people over a 24-hour period will keep you awake for days. And the fact that he let the rest of the world tumble into madness at the same time shows that he went for both the macroscopic and microscopic level of sadism. Arguably the cruelest thing he did to those six people was to briefly give them back their minds in the middle of his sick game. When one of his victims demanded to know why he was torturing them, this was his response:
John Dee:Because I can.
This is useful in showing Dream's moral compass: he doesn't care that much, just wanting his stuff back and returning Dee to Arkham. It's also evidence of how The Sandman is not your typical comic. Dream doesn't have a heroic spaz attack, he doesn't beat up Dee, he doesn't even punish him. When it's all over, he gives Dee back the power to sleep. Dee once again becomes an old, addled man in an asylum. He may not have been redeemed, but he's not a monster either, even though even your most depraved villains seldom hold a candle to what he did.
Secret Six: Vandal Savage, being an immortal villain, has had several millennia and hundreds, if not possibly thousands, of opportunities to cross it, with just a few of the examples we know about listed on his character page. Of those listed, however, perhaps his most disturbing MEH-crossing candidate is setting up his daughter Scandal to be raped because he wants an heir.
Lex Luthor crosses it regularly to show that for all his talk about being humanity's best and trying to protect the world from the alien menace, he's just a petty man who cannot stand the thought of not everyone worshiping the ground he walks on:
In Superman for All Seasons, not only does Luthor brainwash a lady just because she's a fan of Superman, not only does he unleash a plague upon Metropolis that could kill everyone except Superman, but he sets it up so that the only way to cure the plague is for Superman to fly the brainwashed fan around the city to distribute the cure, knowing overexposure to the plague will certainly kill her, and when she does die Luthor blames Superman for her death.
In The Death of Superman, the only notable thing Lex Luthor does in the whole arc is murder his fitness instructor with his bare hands because she managed to land a punch on him, and to see if he can get away with it now that Superman is dead.
Lex gives a few thousand people superpowers in 52, then takes them away again — while they're in mid-flight — because he's pissed that the power-giving treatment won't work for him. Luthor's a sociopath, sure, but he's not usually that petty (okay, there was that one time he stole forty cakes...). The real reason is actually far worse. He thinks that Supernova is Superman in disguise (he's actually Booster Gold) and so creates the situation just to test him, reasoning that Superman will use his powers to save the people. In other words, he kills thousands to test a hunch. It doesn't even work — while Supernova saves as many people as he can, it doesn't help Lex or anyone else closer to figuring out Supernova's ID.
At the climax of The Black Ring, Luthor obtains Reality Warper powers and uses them to heal all strife in the universe. And not in a creepy way either, in a way that appears genuinely therapeutic and helpful. As an example, one panel shows Highfather and Darkseid reconciling. However, Luthor learns the one drawback of his powers is that he cannot use them to hurt anyone, like Superman. Superman begs him not to do anything, offering himself up to Luthor as long as Luthor doesn't ruin this, but Luthor cannot handle the idea of his foe being happy and tries to attack him, ruining the one chance to heal the universe.
In Elseworld's Finest: Supergirl & Batgirl, Luthor crosses it when it is revealed that he murdered Supergirl's baby cousin, and he feels absolutely no remorse because "it was only an alien", not a person.
Mongul II, the son of the original Mongul, kickstarted his career as his father's successor by punching his own sister's head off to eliminate any in-family competition. He only gets worse from there, until he tries to take control of the Sinestro Corps in a coup and is imprisoned in the Central Power Battery by Sinestro himself for it.
In New Krypton, Reactron crosses it in his first appearance when he kills Supergirl's father while threatening to sexually assault her. General Lane does it when he transforms his daughter Lucy into a superweapon, while Lucy herself does when she murders a scientist for the crime of reporting her unstable condition to her father.
In Superman Smashes the Klan, Matt Riggs crosses it when he turns his gun on Chuck (his own nephew) for standing up to him.
Teen Titans: Cheshire crossed the line when she nuked Qurac as part of her plan to extort the nations of the world. Gail Simone outright called Cheshire a monster due to this act and rarely writes her as anything else.
Cheshire:I decided to make a point. America? No, that'd incur too much wrath. And I like shopping there. Russia? They're suffering enough as is. England? Maybe we're all sick of hearing of Di and Fergie, but maybe not...I COULD blow up a little out of the way island, but that wouldn't get the point across...Then I realize...the terrorist capital of the world. That little eyesore, Qurac. Oh, sure, you'll all rage and complain, but inside? You'll be THANKING me.
Even with the above, there were those who argued she still wasn't that bad because she obviously cared about her daughter Lian. So Cheshire crossed the line again in Villains United after Lian's wellbeing is threatened to make Cheshire join the Secret Six. After assessing Catman's heroic attributes and prime physical condition, she seduced him in order to conceive a replacement for Lian, thereby no longer having to care about her or the rest of the Six. Even an amoral sociopath like Deadshot cared more about his own daughter's life and was disgusted by Cheshire's callous disregard. This moment only further cemented she was beyond redemption no matter what she did.
Cheshire: [Mockingbird] may kill my beloved child. So isn't it fortunate... that I'll soon have a replacement?
Amanda Waller is nothing if not incredibly ruthless in her rivalry with metahumans, but she definitely crossed the line in the "Tour: Atlantis" issue B-story "Just When You Thought It Was Safe To Go Back In The Water", where it is revealed at the end that she is behind the spore infections, as she has Dolphin kidnapped and infected with one. She is only too pleased to ruin the reputation of the superhuman community, even if it will destroy the planet in the process. She vaults further across the line later in the event when she arranges the murder of Beast Boy, who was mind raped under her orders into attacking Earth while in the form of Starro, using another innocent metahuman as the weapon. Both die in the process, and this was directly after Beast Boy had just saved the entire planet from an alien attack, including Waller herself. All just to sow mistrust in superheroes, by blaming them for an attack that she actually orchestrated herself.
