Originally justified in Legion of Super-Heroes (pre-Crisis) with Roxxas, the murderer of Element Lad's race the Trommites. Upon being about to be killed by Element Lad, Roxxas is confronted by, and terrified by the ghosts of all his victims. The Legion realize that it would be a greater punishment to leave him alive. The trope is eventually maintained once Roxxas gets over his fears, is driven insane, and goes on another mass murder spree.
Manhunter (the one who's a working mother, and former prosecutor) began her career as a superhero because she's sick of this trope. Her successful kills include Copperhead (who escaped the death penalty under being not guilty by reasons of genetic anamoly), Monocle, and Dr. Moon. She decided not to kill Shadow Thief, on the basis that she wanted to give the criminal justice system a chance to actually work.
In John Ostrander's writing of The Spectre, his human host (Jim Corrigan) asks Father Cramer why the Spectre never responded to the murder of Coastal City. Father Cramer suggested that the Spectre was designed by God only to respond to certain cries for vengeance.
Superman deals with this trope as well. Lex Luthor for example, despite being a Badass Normal, has long been so embedded into the Superman mythos, that he escapes virtually any hairy situation he gets into. Other Superman villains with varying degrees of Joker immunity might be Brainiac, Mr. Mxyzptlk, The Toyman, Zod and Metallo.
Why can't Superman just send Lex Luthor to the Phantom Zone to prevent him escaping from prison? Luthor's crimes occur under Earth's jurisdiction, and whenever Luthor stands trial in American courtrooms, he must serve his sentence in American prisons, and in order to be banished to the Phantom Zone, he would have to commit an intergalactic crime against other galaxies or even the universe.
Superman: Why is it that the good villains never die? Batman: Clark, what the hell are "good villains"?
Prior to Darkseid's death in Final Crisis, the villain seemed to be an apt representation of this trope. One time when the Hal Jordan The Spectre "killed" Darkseid, the villain was instantly resurrected. The suggested implication was that Darkseid was a universal necessity needed to represent evil.
Originally this trope was averted with major DC villains such as the Phantom Zone kryptonians, and Sinestro were killed off by their heroic counterparts Superman, and Green Lantern (Hal Jordan). Eventually, it was reversed when continuity was retconned to establish that the villains were actually not killed.
In the New 52 universe, heroes such as Wonder Woman, Aquaman, Superman, and Hal Jordan seem to be fine with killing alien invaders in battle. Nevertheless, human villains such as Joker and Deathstroke continue to remain at large.
"There's a reason I don't have a list of villains as long as Bruce's, Barry's, or even yours. When I deal with them, I deal with them."
That said, there is one straight example (barring outright Gods like Ares or Circe, who are usually above her weight-class; a "victory" against them usually consists of convincing them to leave humanity alone for a few months) among her villains: the Depraved Dwarf Dr. Psycho. This is a guy with zero interest in reforming, very deadly Psychic Powers, and an oh-so-breakable human body; he's survived so long mostly because he's usually The Heavy in some other Big Bad's scheme, and is smart enough to get the hell out of dodge before or shortly after Wonder Woman discovers his involvement.
In Wonder Woman (1987)Cheetah gets put through the wringer and is presumed dead on numerous occasions, but every new writer on the book brought her back usually with nary an explanation.
Owlman in Dark Nights: Death Metal outright weaponizes this trope: because the concept of Owlman, the evil counterpart of Batman from Earth-3 keeps being revived no matter how often the universe is wiped out or destroyed, he knows he'll always come back. So he has no hesitation in blowing himself up to take a buttload of Dark Multiverse Batmen up, who are far less iconic and won't likely come back. The knowledge also cures his nihilism by giving him an eternal purpose of being the evil universe duplicate of the Dark Knight.
Like most comic book arch-enemies, Black Manta will only seem to be dead or otherwise incapacitated before returning when Aquaman least expects it. He's survived multiple drowning attempts, having his suit ripped open, being turned into a literal manta man, and having his face bitten off and come out no worse for wear.
