In the "Showdown" episode, the genocidal eco-terrorist Ra's Al Ghul purposely punishes and leaves for the authorities his second-in-command Arkady Duvall, because of Duvall's cruel and presumptuous treatment of their henchmen. Arkady treats them like slaves; Ra's, ever the forward thinking, pays them a fair wage and is aiming to strike a blow at the corrupt forces running the railroads. Work ethics and civility are, in fact, among the things on Ra's top ten list of "Virtues to uphold when I become king of the world".
It goes even further at the end of the episode, when it is revealed that Arkady Duvall is Ra's' own son and that Ra's went out of his way to rescue an aged-beyond-his-years Arkady from a third-rate rest-home because "What father can ever forget his son?"
Harley Quinn is perfectly fine with the Joker blowing up Gotham, but she's unwilling to let her "friends" from Arkham (other criminals and psychos) and, even more importantly, her pet hyenas die.
In one "It's Never Too Late", Rupert Thorne invites rival mob boss Arnold Stromwell to "negotiations" in a plot to kill him. Stromwell comes to the meeting because his son, Joey, had gone missing shortly before he received the invitation. When Stromwell asks Thorne what he did to his son and what he wants in exchange for Joey's release, a bewildered Thorne says, "What? I don't target family!" It turns out that Thorne had nothing to do with Joey's disappearance... but Thorne proceeds to try to go through with his plan to leave the missing young man fatherless.
At least one of Thorne's thugs has standards too. As a pair of thugs are carrying Robin to throw him to his death off a bridge, one remarks that he used to fish there as a kid but can't now because there's too much trash (emphasizing this as they throw Robin). At first it seems like a witty insult, but after the deed's done the guy continues to complain about the garbage in the river and litterbugs in general, remarking that they're disgusting.
There's also the case of Victor Fries' reaction to Grant Walker, who specifically wants Mister Freeze to replicate the mutation onto him — Fries/Freeze is appalled at someone intentionally trying to render themselves like him. Bear in mind Freeze claims to be dead to emotions, and he has no fondness for Walker whatsoever (in fact, as the episode goes on, Freeze keeps findingmore and more reasonsto despise him) but he's still human enough to see his condition as a Fate Worse than Death that he wouldn't even wish upon his worst enemy.
In "Almost Got 'Im", The Joker's plan to throw Catwoman alive into a meat grinder and make her into cat food evokes this from Poison Ivy, Croc, The Penguin, and Two-face. No words are said, but their faces say it all◊. And Croc is actually Batman in disguise, so he is even angrier.
In "The Cape and Cowl Conspiracy", Josiah Wormwood reveals a woman Chained to a Railway with a train approaching and tells Batman to surrender. Batman gets to the woman in time, but she turns out to be a hologram. Wormwood asks if Batman thought he would really do it.
Even though The Penguin hates Two-Face and would kill for a chance to kill the guy once and for all, when asked if he was the one who kidnapped Two-Face from the hospital he denies it, stating that "plucking a rogue from their hospital bed just isn't right".
In "Joker's Millions", the Clown Prince of Crime, the person who would happily cause any sort of chaos or destruction if he felt in the mood, absolutely refuses to mess with the I.R.S., and, in spite of the massive tax bill he's saddle with, is quick to try and fork up the cash. He may be crazy to take on Batman, but the I.R.S.? No thank you!
In Secret Society, though Clayface is more bitter it was done to him than anything else, he still remarks on how twisted it was of Morgan Edge to trap him in biohazard barrels and keep him like a trophy. Even Psycho for Hire Killer Frost agrees it was messed up.
Clayface: What kind of guy would lock somebody up and keep him like he was property? Killer Frost: Edge was sick, honey. Buy you don't have to worry about him anymore. Nobody has to.
The Flash ends up in a Christmas truce with the Ultra-Humanite, a supervillain, in donating toys to orphans. When the Humanite offers to repair and 'improve' a gift he accidentally broke, the Flash suspiciously asks if this means it's going to blow up when activated. The Humanite's only response is "Flash... it is Christmas."
To be clear, he not only fixed it, but programmed the normally obnoxious toy to tell Christmas stories in his voice. And helped Flash deliver it to the orphanage/foster home.
What's more, the Ultra-Humanite is Wicked Cultured and Affably Evil; the only reason Flash ran across him was because he was planning on blowing up a modern art museum… on Christmas, when nobody, not even a single guard, would be inside to get hurt.
Hilariously parodied in "The Great Brain Robbery", when Flash and Lex have switched bodies:
(Dr. Polaris and "Lex" are in the bathroom of Legion of Doom headquarters, and "Lex" has just come out of a toilet stall) Dr. Polaris: (as "Lex" is walking out of the bathroom) Aren't you going to wash your hands? "Lex": No! Cuz' I'm evil. Dr. Polaris: (stares in shock)
Played straight in the Grand Finale "Destroyer", when the surviving members of the Legion of Doom warn the Justice League about Darkseid planning to destroy Earth, and also want to help (to the point they'll fight the Justice League if they want to put the Legion in jail, until Batman intervenes). Subverted with Lex, who doesn't care about the world being destroyed as long as he gets revenge on Darkseid.
In the time travel episode, the message from the Vandal Savage of the present to the Vandal Savage of World War II includes a note that he has to get rid of "that raving lunatic" Adolf Hitler. Though arguably this is not so much a matter of principles as a matter of recognizing that Hitler is not, as commonly misbelieved, a master tactician and general, and so his leadership only impairs the Nazi war effort.
Leads to Nice Job Fixing It, Villain when 1940s Vandal only freezes Hitler, who is thawed out and immediately goes on to lose the war for the Axis powers once Vandal Savage is removed from power.
In his final episode in the series, "Hereafter", Vandal Savage does openly admit he went too far with his last scheme at world conquest and deserves to be punished. And this is after he's lost a bit of his sanity.
He does a good job remaining calm, but in "Twilight", it's rather clear that even Darkseid is horrified by what Brainiac's arrival means for his planet.
◊. And Croc is actually Batman in disguise, so he is even angrier.
