In Gregory Horror Show the series has a character named "Judgement Boy" where he will ask the Guests a question, regardless of relevance, and tells the consequences of the choice after the judgement is passed.
In Monster, it's gradually revealed that Johan and Anna's mother was forced to give up only one of the twins to the sadistic Bonaparta as part of a psychological experiment. In an attempt to hide from them, she had told her neighbors that she only had a daughter, and made Johan (who seemed sane back then) wear a wig and dress to impersonate Anna whenever he left the house. When Bonaparta and his men found Mrs. Liebert, little Johan was still wearing his disguise, so it was impossible to tell which child she let them take away (although it's already known that this was Anna).
What makes it even worse? The fact that Mrs. Liebert was able to make a decision between the two of them at all is part of what helped shape Johan's personality.
At the end of the series Johan presents Dr. Tenma a sadistic choice. Either Tenma sacrifices his main value of Thou Shalt Not Kill by shooting Johan or Johan kills a little boy. Thankfully a timely intervention from a Papa Wolf spares Tenma from having to make that choice.
In Digimon Adventure 02, the Digimon Kaiser forces Daisuke to choose which one of his four teammates won't be eaten by a three-headed digimon. When time runs out, Daisuke offers himselfin place of them, but then all his teammates show up — the tied-up kids were only shapeshifting digimon.
Kannazuki no Miko - The priestess sacrifice ritual is essentially this without having a third person between the two, instead they have to decide amongst themselves.
Has happened many times in Mazinger Z: Often Baron Ashura held someone hostage and threatened to kill him or her if Kouji did not surrender, but there were different instances:
In episode 17, Big Bad Dr. Hell crafted a Mechanical Beast could set earthquakes off. After using it to bring down several Japanese cities, The Dragon Baron Ashura threatened with obliterating Tokyo unless Dr. Hell was appointed director of Photonic Research Institute. If the heroes gave in, Dr. Hell would have full and unopposed access and control to the lodes the Japanium was extracted from and plans to build his own Photon Atomic engines, and nobody would be able to stop him from taking over the world. If they did not agree, Tokyo would become a giant hole in the ground.
In episode 18, a Mechanical Monster cuts a passenger ship in half. A woman reaches a lifeboat but her mother has been caught in one of the whirlpools formed by the sinking ship. If she stays away, her mother will die. If she comes closer, maybe both of them will die. At the end her mother chose for her. She shoved the boat away her. She drowned, but she managed to save her daughter's life.
In episode 31, Dr. Hell kidnapped three men, hypnotized them in piloting three of his Mechanical Beasts and ordered them to attack Mazinger-Z. Thus, Kouji found himself severely limited, since if he attacked full-force, the prisoners could die.
In episode 61, Lorelei, a little girl his little brother was infatuated with, fused with a Robeast and challenged Mazinger-Z. She could not be split from the robot, and if Kouji fought, he would kill her and would break his brother's heart. Finally Kouji had to fight, and Lorelei died.
It also was a very common occurrence in the sequels. In one of the Great Mazinger manga chapters a Warrior Monster was holding Jun hostage. Tetsuya did not dare to attack the Monster, but Prof. Kabuto ordered him throwing his doubt out and attacking (in spite of Jun was his adoptive sister, Battle Couple and Love Interest). In another of the manga versions, Great Marshall of Hell -Big Bad's second The Dragon- blew up one city and threatened with destroying Tokyo as well, unless the Japanese Government destroyed the Fortress of Science and all Humongous Mecha stored there. The Government gave in and destroyed the Fortress. Great Marshall turned Tokyo into a wasteland nonetheless.
UFO Robo Grendizer: In one manga chapter, Duke gets attacked by one of his oldest friends, whom he believed dead but was being mind-controlled by the Vegans. His friend could not control his body but he still could warn Duke stay away from him... and beg kill him.
In Trigun, the villain Legato Bluesummers forces the main character Vash into making a choice between killing him and thus renouncing everything that he based his life on, or letting his companions die, as Legato is mentally controlling a group of people about to kill them. He kills Legato, saving his companions, and then sinks into a Heroic BSOD in the next episode.
A variation in Full Metal Panic!: Sousuke finds himself in what is obviously a crooked hostage situation, with the terrorists holding his classmate Chidori and his commander Tessa. When they ask him which of the women to release first, he mentally weighs the choices (Chidori gets priority as per SOP, but he was concerned that the clumsy Tessa would be unable to get to safety if things got rough) and ends up having them send Tessa. The whole thing went to pot regardless...
In the fourth arc of Umineko no Naku Koro ni, Kinzo Ushiromiya decides he's going to test which of his grandchildren is most worthy to become his successor as head of the family. The contents of the test, you ask? "In order to gain two, sacrifice one." A) Your Life B) Your lover's life C) everyone else's lives. George and Jessica actually do make somewhat shocking (albeit convincing) choices with their own brand of justification...only to take the bad guy by surprise by deciding to sacrifice none of the above and fightingback instead. But this being Umineko, they die horribly anyway.
This is then averted in the seventh novel where its shown the test was used again by Kyrie and Rudolf but only to lure the cousins to where they would be killed one by one.
In chapter 101 of the manga and the second series, Roy Mustang was forced to choose between letting his Lancer, Hawkeye, die in front of him (she had her throat slit open and was bleeding to death) or opening the Gate in order to complete the evil guys' plans. She persuades him not to co-operate through her eye signals. Luckily, she is saved anyway with a little bit of Xingese alchemy and chimera powers. Not so luckily, Pride then decides to dispense with the "Choice" part of the trope and forces Roy through the Gate anyway.
Also in the manga and Brotherhood, the Homunculi give Dr Marcoh the choice of agreeing to help out the homunculi and being complicit in whatever horrible plans they have in store for Amestris, or resisting and watching the village where he worked as the town doctor get wiped off the map. The homunculi even try to stop him from taking a third option though killing himself, as suicide will only result in the destruction of said village. Luckily, Scar shows up, which allows Marcoh to take a FOURTH option, where Scar stages the murder of Marcoh and helps him escape.
In Bleach, Orihime Inoue is forced to work for Aizen in order to save the lives of her friends, who don't even know they are being held hostage. To make things even worse, Aizen later reveals that the only reason he kidnapped her was to lure her friends and the The Cavalry into a trap.
Also in the backstory Soul Society has (twice, counting filler) been forced to make a difficult decision: wipe out a certain race/group of people, effectively committing genocide, or stand aside and allow the race/group in question inadvertently destroy reality with their unique powers. Both times, they were forced to choose the former.
Soichiro Yagami of Death Note is forced to decide between allowing his daughter Sayu to be killed and giving the responsible organization a weapon of effortless mass murder.
Later on, as Mello continues to blackmail him, he's forced to choose between the death of Sayu or revealing the identity of the second L, who happens to be his son Light. Matsuda gets him out of that one.
Also, Light indirectly forces Rem to choose between letting her protegee and partner Misa die or killing L to protect her, knowing that it would result in her own death. She chose the latter.
In D.C. II SS as part of the main plot, Otome Asakura turn into Heroic BSOD as she was forced to choose between saving everybody in the entire island by withering up the tree that would cause her love, the main protagonist Yoshiyuki Sakurai, to vanish from existence, or sit back doing nothing and stay with her love till the end, leaving the tree go rampant that could potentially cause the end of the world.
At the breaking point that after the creator of the tree Sakura Yoshino and Otomes' grandfather vanished in two ill-fated attempts to keep the tree under control, Yoshiyuki finally being told the tale of his origin. Aware of his fate if the tree withered, he convinced Otome that stopping the tree is the only option. There were no third option, Otome wither up the tree. Eventually Yoshiyuki vanishs in an extremely tragic way.
Mentioned in Naruto, when Kakashi is giving Team 7 their Secret Test of Character and he asks Sakura what she would do if he threatened to kill Sasuke unless she kills Naruto.
Much later we find out this actually happened to Nagato after Hanzo attacked his group out of paranoia: he had to kill Yahiko or else Hanzo would kill Konan. When Nagato freezes up at the thought of hurting either of his friends, Yahikotakes a third option: he grabs the arm the chooser was holding a kunai in and stabs himself with it. Nagato then became a Dark Messiah. Konan helped.
Also, Sasuke by his post-Itachi-killing activities (joining Akatsuki, attacking the Raikage's brother, and attacking all the other Kage at the summit) made himself an enemy of the whole ninja world. Even Naruto's friends have decided to kill him, leaving Naruto stuck between breaking his word or pissing off the whole ninja world.
And Itachi was faced with the most agonizing choice of them all. His Clan was planning a coup against Konoha, one that would potentially spark a new Great Ninja War. Thus he was faced with a terrible dilemma; stay loyal to his clan and ultimately be responsible for the deaths of thousands of innocents, including probably the whole clan in the end anyway, or massacre his entire family, down to the last child. He couldn't bring himself to kill Sasuke, though, so he did his best to make sure he hated him completely and would never suspect the truth, so he would be allowed to live.
Both Itachi's and Nagato's choices were set up by Shimura Danzo, who utterly loves this kind of shit. He worked together with Hanzo to destroy the original Akatsuki, because oh boy, peace and understanding is a seriously pernicious philosophy when backed by ninjutsu. Then he took one of his ANBU commanders and used him to utterly neuter the threat of the Uchiha for all time, at the cost of destroying the boy and sacrificing a large number of civilians for the crime of being Uchiha. And creating the hate-monster known as Sasuke. Who killed him, so at least consequences eventually hit home.note Nagato crushed Konoha to the ground, but Danzo personally profiteered from that attack and got himself appointed Hokage for all of a couple of days.
To cap it, Itachi was still reporting to Danzo the entire time he was in Akatsuki. (Which Danzo had turned into an evil league of evil to begin with.) He wasn't a nuke-nin, he was ANBU in super-deep cover that he only broke seconds before he died. Somebody was raised to be a very good tool indeed.
He's still protecting Konoha once he comes back as a confetti zombie, although admittedly he's only free to do so due to a time-delayed hypnosis he embedded in Naruto to compel Sasuke to go home and rejoin the village, which he had not anticipated having the posthumous opportunity t trigger himself. Still, he treats this accidental auto-hypnosis as an opportunity to follow his own will instead of zombie-master Kabuto's, so I think it's safe to categorize him as psychotically loyal.
In One Piece, Pirate Empress Boa Hancock, believing all men to be bastards imposes such a choice on Luffy. Either she'd save the amazons she turned to stone or allow him to leave the island. For Luffy picking the life of someone he befriended just five minutes ago before his own isn't really a choice. His lack of hesitation even caused her to have a Heel-Face Turn.
Nami's adopted mother Bellemere is a real Tear Jerker of a borderline case, given that Arlong couldn't have understood fully at the time he was forcing her into a Sadistic Choice between acknowledging that Nojiko and Nami were her children and being shot for not having enough money to pay the extortion fee for all three of them. However, it was made pretty clear in the manga that to Bellemere, this was a sadistic choice: she and Nami had fought earlier over the mother/daughter issue, and this being a manga where even the cuddly little reindeer is a Hot-Blooded Determinator, refusing to acknowledge Nami and Nojiko as her children was not an option in her mind. Possibly Honor Before Reason, but Bellemere is still a certified Badass.
It is also pointed out that Arlong would be demanding money again anyway, so her action is actually smarter than it appears... Plus, Arlong and his crew demolished all of the seaworthy vessels on the island before attacking, which would have left Nami and Nojiko with no way to escape the island, making it only a matter of time before they got caught and assuredly killed. It was heavily implied(if not outright stated) that Bellemere had already realized this was the case.
Arlong gives another Sadistic Choice to Nami after his Loophole Abuse to get out of their bargain provokes the whole island to attack: either submit to be his slave forever and have the villagers spared, or attempt to fight and have him kill everyone except her, and have him enslave her anyway. And either way, he'll kill the Straw Hats for attacking him. Nami, after some consideration, chooses the second option…and fortunately for her, that's when Luffy wakes up.
Another backstory of a Straw Hat, involved Franky's own adopted father Tom, given the choice of using his trial to pardon himself of the crime of building the Oro Jackson, the ship that would later come under the posession of the late Pirate King, Gold Roger and his pirate crew; or request that Cutty Flam (Franky) is pardoned for creating the ships that were used to attack Water 7, and frame him due to the scheming of Dirty Coward Spandam for the Pluton blueprints. Tom not only chose the latter to protect Cutty Flam, but earlier declared proudly that he, indeed, created the Oro Jackson, and is not the least bit ashamed of it. This doubled as a final lesson to teach Cutty Flam, as he previously denied having created the ships that attacked Water 7. Even the judge felt bad about sentencing Tom, and it was an incident that Franky could never forgive himself for allowing to happen, and nearly killed himself trying to stop the Puffing Tom ironically sending its creator, and Franky's father figure to the Judicial Island to be sentenced to death. This is what led him to become Franky in the first place...
It also happens to Doflamingo when he is given this ultimatum: either quit being a Warlord and get Caesar Clown back while bringing down the wrath of the Marines, or keep being a Warlord but bringing down the wrath of Kaido of the Four Emperors for no longer being able to provide him with the Smiles Caesar helps produce, he chooses to Take a Third Option: he fakes quittiing being a Warlord in order to lure Law and the Straw Hats into a trap.
Luffy of all people pulls this on Zoro when they first meet! To explain, Zoro first appears being held at a Navy base by a tyrannical Captain and his spoiled son who have turned the base and island into their own private kingdom. The Marines are about to kill Zoro when Luffy lays down the line; either be a lawful citizen and be killed, or fight back and be labeled a criminal. This is actually better than the 'agreement' Luffy decided on earlier- The captain's son has Zoro's swords, so if Luffy gets the swords, Zoro will have to work for him to get his swords back!
Zoro: You must be demon spawn...But I'm not ready to die without a fight! All right, dammit! You've got yourself a pirate!!
Shows up as a Secret Test of Character in Hunter × Hunter: who would you save, your wife or your mother, if you could only save one of them? The correct answer is silence, as there is no right answer.
Though the super secret bonus answer is understanding that you might one day have to make a choice like that for real.
Shows up again during the Hunter Exam, when the main characters are tasked with reaching the bottom of a giant tower within a certain amount of time. The last obstacle is to choose between two paths: a short path that requires the group to leave behind two members, ensuring that they fail the exam, or the take the long route that they don't have anywhere near enough time to take. The final decision: Take the long route...and then smash through the wall dividing the two routes to get on the short one instead.
It ends up being the third choice being taken: Nagi willingly smashes the stone in defiance of her grandfather, despite knowing nothing - only that he was horribly worried about something very important for him, and the stone smashing would solve it. In thanks, he's promised to protect her at her insistence.
When losing combat against Jolyne, he forces her to choose between killing him and saving the disc that contains her father's memories.
He forces Jotaro to decide, in a split second, between killing Pucci to save the world and letting his daughter die, and saving his daughter but dooming the world. He tries to Take a Third Option and do both, but it doesn't work.
Yu-Gi-Oh!: When Yami Marik and the Pharaoh duel in the Battle City finals, the loser would lose their other half (Either Marik or Yugi, obviously.) Luckily, Pharaoh is able to swap the two Marik's souls and get Yami Marik banished, so both of them are safe.
Regular Yugi's duel with the Brainwashed and Crazy Joey, which is set up in such a way that he can't take a third option or someone (either him, Joey, or a kidnapped Tea) will die. He chooses to set himself up for death and save Joey and Tea. Which is followed by Joey setting himself up to die to try saving him. Luckily, either Kaiba (manga) or Serenity (anime) finish the deal.
This started back at season one, with the Yami Yugi's duel against Kaiba. Lose your dual and star-chips or win and possibly kill Kaiba. After all, card games areSerious Business.
Not that Yami had any issues with this. If it weren't for Yugi being more aware of everything by that point, Yami would've quite cheerfully let Kaiba die.
In the middle of the final battle between Dartz and Yami Yugi and Kaiba, the Orichalcos Knights are the souls of Yugi, Jonouchi, Mai, and Pegasus, and if our heroes attack any of them, then the soul would be dead forever.
Unfortunately for Dartz, this causes something he didn't count on. Pegasus is able to use the opportunity to get a message to Yugi about how to use a card that is vital to victory. In other words, Nice Job Fixing It, Villain.
In Fruits Basket, Akito finds out that Haru and Rin are in a relationship and asks Rin which of the two of them started it. The implication is that Akito will hurt whoever began it, so Rin can either tell the truth that it was Haru and escape punishment but live with the guilt of Haru being hurt, or lie, take the blame, and be hurt herself. She wastes no time in lying, and is pushed out a window. Given that it's Akito, it's entirely possible that both would have been punished if Haru was blamed, since Akito hated Rin because not only she's defying the leader openly, she looks like Akito's mother, Ren.
in Rave Master when a super weapon is activated Musica has the choice of letting it fire and killing his companions or letting Reina, the evil general who only just became good, sacrifice herself to destroy it. The choice is no less obvious having read the build-up, but it's still treated like a very hard one for him.
Averted and Subverted at the same time in Naruto. Minato, after making the Big Bad run with his tails between his legs for the moment, is faced with two choices: 1. Let Kushina seal the Kyuubi inside herself again and kill it even though it will just revive itself in the near future, anyway. Thus, saving Konoha and Minato, along with their baby in the short term. 2. Seal the Kyuubi inside their son, essentially offering their son up as a sacrificial lamb for a Bijuu, effectively making him the next Jinchuuriki ,saving Konoha and the rest of the world in the long term. Minato chose the latter.
Subverted in that it's not such a bad decision since Minato also plans to seal the rest of their chakras inside Naruto so that they can meet him again in the future. Minato's choice eventually paid off.
In the manga, Judai is forced to duel Sho, as Judai has failed every test since getting in, and Sho got a 0 on his last test. If Judai wins, Sho will be expelled and if Sho wins, Judai's deck, which he got from his friend and mentor Koyo Hibiki, will be confiscated. When Sho gets the upper hand, Judai considers losing, but decides to go for his victory instead, and it turns out that Sho did not actually get a 0 as his final grade; the computer simply marked the test as zero due to an error (a very common error, in fact) because he didn't write his name on the test (as Midori reports to Chronos while chastizing him for arranging it), so he does not get expelled. Later on, Midori gets one during her duel with Reggie, who tells her that if she wins, Reggie will fall into a coma and be unable to give her information on awakening her brother Koyo from his Shadow Game induced coma (and the same will happen to her if she loses). Then Judai arrives and Midori has to choose between awakening Koyo and saving Jaden from having to face Reggie in a shadow game, and chooses the latter. She fails, and learns that Reggie does not, in fact, know how to awaken Koyo, before also going into a coma.
Another version of the Trope occurs in Season Three of the anime. During Judai's Disclosure Duel with Professor Saito, Professor Cobra traps Asuka in a Drowning Pit and threatens to let her drown if Judai wins the duel. Unfortunately, losing might put the entire school in a lethal situation. Fortunately, while Judai isn't able to Take a Third Option here (other than stalling against Saito, who eventually tries to TakeHimWithHim, Jim manages to find and rescue Asuka in time, letting Judai win by protecting himself from the damage from Saito's kamikaze strike.
In Mon Colle Knights, Redda provides two nasty ones to Mondo; first, he demands that either Mondo give him the Monmon items or he kill Rockna with his sword (which turns out to be a rat in disguise, with the real Rockna held captive by the Terror Dragon). Next, he tells Mondo that he can either get destroyed by the Terror Dragon while trying to save Rockna, or destroy the dragon and her with it. However, with Redda away after his monster friends were sucked into a wormhole, Zaha arrives just in time to save Mondo and help rescue Rockna in time to destroy the dragon (even though it comes back later).
A Certain Magical Index actually gives a villain one of these. After Ridovia's plan to use a religious artifact to forcibly convert Academy City to Roman Catholicism fails, she tries to make a getaway in a private jet, only for Laura Stewart to catch up with her, blowing out the door to the plane so she gets sucked out, along with the artifact and a worker on the plane. She's then given a choice while in freefall between saving the artifact or the worker (herself being a Well-Intentioned Extremist who tries to save innocent lives.) She tries to do both, and the scene cuts off before showing if she succeeded or not.
In Tokyo Ghoul, Yamori presents Kaneki with one after physical torture fails to break him. He learns the hostages he sacrificed himself to protect were never freed, and Yamori orders him to choose whether he will kill a mother or her young son. Kaneki refuses to choose, and pleads for the villain to kill him instead. This, combined with Nico expressing his distaste for his boss's actions, enrages Yamori to the point that he strangles the child to death and then kills the mother. It acts as the proverbial final straw, sending Kaneki over the Despair Event Horizon and triggering his descent into Anti-Hero territory.
The anime adaptation changes it to a pair of lovers that had helped tend to Kaneki during his imprisonment, to equally brutal results.