Villains are meant to be punished, but sometimes things get too intense. Superheroes are supposed to be the good guys, and when they start just murdering their adversaries it undermines the premise. The late 80s and 90s are known for heroes who broke spines, trapped villains in Jigsaw-like conundrums, and otherwise confused "mature" with "gratuitous." Strangely, though, heroes who execute their villains go all the way back to the Golden Age of comics. With roots in pulp characters like The Shadow and The Spider it's not really surprising, just disturbing. In every era even funny characters have sometimes committed some pretty grim murders.
10 Plastic Man Asphyxiates a Pathetic Giant
Cyrus Smythe is best described as an alchemist, searching for eternal life. He... achieved it? Police Comics #11 told Smythe's story where his body died in the 17th century but his disembodied brain survived and went crazy. In 1942 he manages to get inside of another body, and puts his alchemical wisdom to weird use. His potions let him grow hundreds of feet tall, but his legs don't grow with his body. He walks around on his hands, terrifying and bewildering the populace and triggering a battle with Plastic Man.
In 1942, Plastic Man was an even less serious character. It was utterly shocking when Smythe appeared to eat the erstwhile "Eel" O'Brien. Much worse, though, was Plastic Man's response. He expanded in the giant's windpipe, asphyxiating the sad monster and apparently killing his brain for reals.
9 Batman #1: Batman Hangs a Different Pathetic Giant
The early 1940s were hard on comic book giants. Batman #1, not the Dark Knight's first appearance, saw a number of firsts.The Joker's first appearance, Catwoman's, the Batplane's, and even the first version of Batman's origin. It wasn't the home of Batman's first kill, but one of the most memorable.
"The Giants of Dr. Hugo Strange" is exactly the story it sounds like. Hugo Strange turns several mental patients into 15-foot tall giants in an effort to overwhelm Gotham's police. Batman intervenes and, in a chilling scene, wraps a cable dangling from the Batplane around an attacking giant's throat. With the corpse dangling from his vehicle, the Caped Crusader declares "he's better off."
Um, nope, he's dead.
8 Detective Comics #29: "Death... to Doctor Death."
Doctor Death was Batman's first recurring villain. A mad scientist with a monstrous appearance, he showed up much later in Scott Snyder's "Year Zero" Batman reboot. The original was a villain who dealt in diseases and poisons, threatening mass destruction throughout Gotham with his schemes. It's hard to argue that this terrorist didn't deserve some very harsh treatment, but Batman's method of execution is still unsettling. Batman's attempt to apprehend the Doctor sets Death's lab on fire, and Batman traps him in the burning building. As he stands outside, the Dark Knight remorselessly intones "Death... to Doctor Death." It's chilling, more a statement we'd expect from Alan Moore's Rorschach than from today's Batman, well known for his "no fatalities" policy.
7 Scourge Massacres the Bar with No Name
The Bar With No Name is a semi-famous Marvel location, a place where supervillains meet and greet. When a group met to discuss the problem of the murderous vigilante The Scourge of the Underworld, Scourge was secretly the bartender. Scourge killed 18 unarmed and unprepared D-list villains that night, from Firebrand to Turner D. Century. Scourge's identity is still unknown, making him more plot device than character, and the massacre turned out to be a major purge of Marvel's collection of unnecessary characters.
They were villains, but it's still pretty cynical.
6 Marshall Law Hunts Down the Sleepman
The first Marshall Law mini-series (1987) is a superhero deconstruction with some solid satire. Law is a Hero Hunter, basically a Blade Runner who tracks down enhanced super-veterans who can't adjust to life stateside. The main plot involves the Marshall hunting a creepy super rapist called the Sleepman. Law suspects the Sleepman is actually the Public Spirit, a Superman pastiche in a rough draft of Homelander's costume. Sleepman's actually Marshall Law's biggest fan, though, and he fridges Law's fiance to instigate a showdown.
It works. Always gun-happy, Law waits until Sleepman is vulnerable, then shoots him with a special bullet before dropping him in the ocean.
5 Superman Kills a Helpless Zod
Superman is well known for his non-lethal moral compass. Kingdom Come and Superman vs The Elite both offer huge repercussions when society chooses heroes who kill over the Man of Steel. Supes is so powerful that he can usually solve a problem by banishing foes to another dimension or stranding them on an asteroid, but there are exceptions that don't involve Zack Snyder.
In this 1987 story, Zod and his henchmen escape from an alternate Phantom Zone and... Kill. The. Earth. Superman arrives too late to save anyone, but he's immune to their universe's various Kryptonites and obliterates their powers with Gold Kryptonite. The three Kryptonians are now completely helpless, and hurl impotent threats. So Superman produces Green Kryptonite, killing them slowly, as he must have intended from the start.
4 KGBeast's Premature Burial
Another case of Bat-homicide, the 1994 story "Ten Nights of the Beast" features the Soviet super assassin the KGBeast. Beast arrives in Gotham on 10 missions of murder, and the Dynamic Duo tries to stop him. The Beast comes across as an unstoppable force, his plans circumventing any and all preparations made by law enforcement or Bats. Batman is so desperate he kidnaps the PRESIDENT into "protective custody."
This culminates in a sewer showdown, where the Beast expects a manly slugfest. However, Batman has a contingency plan cribbed from Edgar Allen Poe. He locks the Beast behind a steel door, leaving him to die an excruciating death in the dark. It's the closest we'll get to a crossover between Batman and Saw.
3 Punisher Executes Your Friendly Neighborhood Stilt-Man (2007)
Frank "Have Gun, Will Travel" Castle kills people. Probably bad guys, but mostly mobsters and the like. It's rare that plot constraints allow him to put a bullet into a long-running villain. Stilt-Man was never particularly respected, but his armor made him too much for law enforcement to handle, clearing the low bar for supervillainy.
That said, Wilbur Day wanted to reform. He signed up for herohood via Civil War's Superhero Registration Act and approached his work with gusto. He was excited when he and Castle showed up chasing the same target. Then Frankie put a RPG in his crotch and a bullet in his head. The dude's last words were "I surrender." Castle is a mean motor scooter but this is just sociopathy.
2 The JLA Disintegrates Darkseid's Soul (2008)
Batman's Final Crisis murder-duel with Darkseid is pretty well known. The Dark Knight killed the Bad God with a magic bullet, but you can't stop the Lord of Apokalips by just killing his body. So two different Flashes tag-teamed the Black Racer, the New Gods' incarnation of death, leading him to Darkseid's soul while Superman somehow sang the mad god's essence out of existence.
Darkseid was a threat to the universe. The JLA couldn't just take away his laser rifle and stick him in a box. Nonetheless, this was a precisely orchestrated murder conspiracy, executed by heroes. It was also vengeance for Batman's apparent death. Bad form, good guys.
1 Flashpoint Batman Ends the Reverse Flash (2011)
Dr. Thomas Wayne is the avenging Batman of the Flashpoint timeline, where Bruce Wayne was murdered and his father became Batman. He's darker and nastier than his son at his worst, and embraces guns like they're his surviving relatives. That said, sometimes it pays to have someone who will do the dirty work.
In this story, Barry Allen needs to defeat Zoom to save the world, and he loses the fight. Badly. While Zoom is gloating, though, Thomas Wayne remorselessly ends him. In the animated film he shoots Thawne in the head, and in the comic he impales him on an Amazonian sword. In both cases, he does the deed from behind. Zoom was impossible to kill from the front, but it's a clear execution. It's weird that the "bad Batman" commits the most justifiable homicide on the list.