During a flashback in Irredeemable, Qbit is shown asking The Plutonian, a Superman-type superhero, what it's like to have so much power and responsibility. Plutonian doesn't answer, but he's visibly irritated by the question. Years later, after the Plutonian becomes an Ax-CrazyOmnicidal Maniac, he sets out to destroy the entire country of Singapore, and tells Qbit to choose ten people to save out of four million.
In Y: The Last Man, Alter puts a gun to the head of one of the Hartle twins and offers the other a choice — either reveal the location of the last man on Earth or "live the rest of your miserable life knowing you could have saved your sister."
In Garth Ennis's run, The Punisher puts Daredevil through the "choice between ideals" version. The Punisher is out to snipe a vicious mob figure; Daredevil attempts to stop him, insisting that the mob boss needs to be taken out legally, through the justice system. The Punisher manages to incapacitate Daredevil and bind him up with a gun with one bullet in his hands pointed at the Punisher's own head, such that the only way Daredevil could stop the Punisher's vigilante justice would be to violate his own ideals by fatally shooting Punisher himself. Daredevil chooses to pull the trigger, at which point it is revealed that the setup was also a false dilemma: the gun had no firing pin.
In the Joker's Asylum mini-series, the issue focusing on Two-Face has him setting up somebody else with a disfigured face in one of these. He can either shoot Batman (who saved him from dying in a fire) and save his wife from having acid spilled on her face, or save Batman. He tries to Take a Third Option by shooting Two-Face, only to find out that the gun isn't loaded and the person who was supposedly Batman is just one of Two-Face's goons. Although the real Batman comes and rescues everybody, his marriage is ruined by the knowledge that he couldn't choose his wife over Batman. Damn.
That issue also features something of a meta-example: it asks the reader to take a coin and flip it. If the coin comes up heads, the man gets a happy ending where he reunites with his wife, who manages to forgive him, and they rebuild their lives. If it comes up tails, the man fails to do this, succumbs to despair and puts a bullet through his brain. The choice is, knowing you have a 50% chance of dooming this man if you flip the coin, do you flip the coin?
Done to Spider-Man by Harry Osborn, although slightly subverted. Harry had kidnapped Aunt May, Flash Thompson, and Mary Jane, and told Spider-Man that one of them was rigged to a bomb, and the other two were completely safe, urging Peter to save the one most dear to him. That was intended as a clue, as Peter would use the word "dear" to describe Aunt May, but never Flash.
Done in Spider-Man: India as a nod to the movie. The Goblin drops Aunt Maya and Meera Jain off opposite sides of a refinery tower. Spider-Man grabs Maya but doesn't have time to reach MJ...but luckily, Doctor Octopus saves her.
Secret Six: Junior forces victims to choose whether she kills them or their family and friends. If they choose themselves, she kills them. If they choose their family, she kills them anyway and leaves the body and a recording of them begging her to kill their family where the family will find it.
Another variation appeared in the Assault On New Olympus arc in The Incredible Hercules. Hephaestus traps Hercules and his teen partner Amadeus Cho in separate chambers, each with a Big Red Button. The only way for Herc to be free is if Cho pushes his button, which would remove the air from his chamber, killing him. Or Herc can push his button, saving Cho by sacrificing his life. Almost before Hephaestus explains the trap, Herc and Cho push both their buttons simultaneously, shorting out the system and releasing them both. This scene also counts as a Heartwarming Moment, showing that Herc and Cho would each sacrifice themselves for each other, no questions asked. And a Funny Moment because Hephaestus neglected to consider this option and expresses his anger with a succinct "Frickin Hercules".
Ultimate Red Skull was once hired to kill a guy, but instead of just shooting him, he got the guy's wife and infant son, held a gun to the infant's head, and gave the wife a choice — either he kills the baby or she stabs her husband to death with an old pair of scissors. Then after she killed her husband, Red Skull threw the baby out the window anyway, his goons then raping her until well into the next day. Then taking the bread and milk out of the fridge when and his goons eventually left.
Later, as the Red Wasp, she gets a belated revenge.
In Transformers: Last Stand of the Wreckers,Big Bad Overlord offers his prisoners the chance to compete in gladiatorial matches to the death. Anyone who wins twelve matches gets a choice - nobody has ever spoken to somebody who has made it, but knowing that Overlord is Ax-Crazy, the Sadistic part almost goes without saying. The choice? Commit suicide on the spot, or fight Overlord. The two options are one and the same.
One of the rare examples of the hero making the choice and taking the consequences happened in Infinite Crisis where Wonder Woman was faced with either murdering Maxwell Lord in cold blood or allowing a brainwashed Superman to remain under his control. She kills Lord and later hands herself in to the authorities (and is eventually found not guilty as she was acting in self-defense).
She had wrapped her magic lasso around Lord, forcing him to tell the truth and she asked how she could break his mental hold on Superman and he said, under the influence of the lasso, the only way to make him stop was to kill him and CRACK! she snapped his neck without hesitation because she knew it was the only way.
The wolf prince Hrimhari is given the chance to sacrifice his own life to save his love Rahne Sinclair of X-Factor. However, Rahne is pregnant with his child, and the one offering the deal will only save one person in exchange for Hrimhari. One life for one soul. Hrimhari subverts the choice by choosing to save the nearby mortally wounded Elixir instead, since Elixir has extremely powerful healing powers (no Healing Factor though, hence the "mortally wounded" issue) that could save Rahne and the child.
In Astro City, while Superman expy Samaritan is out on a date with feminist hero Winged Victory (herself an expy of Wonder Woman,) he is trying to understand how her philosophy informs her superhero style. He asks her if, faced with a choice between a man and a woman who were in danger, she would always choose to save the woman. Her answer was "All other things being equal — yes."
One Spider-Man annual features the Scorpion doing this to J. Jonah Jameson. Holding Jameson's son John and his wife Marla hostage, the Scorpion demands that Jameson decide which one he kills, saying he'll let the other one live. A broken Jameson subverts this trope when he pleads with the Scorpion to kill him instead, saying that he was the one who turned the Scorpion into a monster. The Scorpion likes the idea, but the trope is Double Subverted when he decides to just kill the entire Jameson family. Fortunately, that's the exact moment when Spider-Man pulls a Big Damn Heroes rescue and interrupts the Scorpion so the Jamesons have time to escape.
In Dark Empire, Luke finds himself before the reborn Emperor, who offers to make him his apprentice. Luke has his lightsaber. But the Emperor has 'survived' by Body Surfing, and he can do this to anyone not trained to resist - and if Luke kills him, there's one extremely powerful Jedi who can't resist right there. Luke kneels at the Emperor's feet, planning to try and sabotage him from within. And he does, to an extent - but this isthe Emperor, and little by little Luke becomes the mask.
One Batman comic has Batman forced to make one of these by causality. He ended up in an alternate universe where there were no heroes at all, not even Greek myths. In this world, Bruce Wayne's parents had yet to be killed, and he had to make a choice: save young Bruce's parents, or let them die and ensure this world had at least one hero in the form of its own Batman. Batman chooses to save the alternate Bruce's parents... and then the trope is subverted: inspired by the memory of the vigilante who saved his family, the alternate Bruce Wayne studies, trains, and on reaching adulthood dons the cape and cowl himself.
Rorschach also waited around outside ostensibly to see what choice the kidnapper made, but this is Rorschach we're talking about here; it doesn't seem likely he'd have let the man survive in any event.