In one episode, a man is given a choice by a terrorist to either allow his son or wife to leave (he's holding them at gunpoint to force him to pick something up for him). After agonizing about it, he picks his son to be released. The terrorist then releases his wife instead, explaining that he only did that to learn who was more important as a hostage.
Nearly the entire first season is a series of Sadistic Choices for Jack.
Several of the tasks have been picking the lesser of two evils. Perhaps the best example came during the China leg of Season 17, Both challenges were "Needle in a Haystack" challenges, and both of the particularly nasty variety. Teams had to pick either finding a boat with specific markings in the Marina or riding a tram and identifying the right signs, if you didn't get the right signs then you had to ride the Tram again and again. At the time the racers got to the leg it was nighttime; with the former challenge, they had to hold their flashlights over the signs one by one and with the latter, they had to search for specific signs in a sea of neon.
Amazing Race 21 features searching for books in Cryllic, or learning a synchronized swimming routine.
Angel: In Season 5 Angel and Spike were given the choice to either sacrifice Fred or let many others die.
Arrow: In Season 2 Oliver is forced to choose between Shado and Sara while on the island. He chose Sara. Later on in the season Slade forces Oliver to once again choose, this time between Moira and Thea. Moira takes the choice into her own hands.
Awake: In the pilot episode, it is suggested to Michael that once he comes to realize which reality is true he will stop dreaming the other. Or, as he put it, once he decides who has died (his wife or his son), he'll never see him/her again.
Sheridan and Delenn (and, by extension, all the lesser species) are compelled to chose between following one of the two uber-races: the (near-)fascist Vorlons and chaotic murderous Shadows, each of which chooses would eventually result in an endless war. They choose not to choose at all.
In a less obvious way Sheridan himself inadvertently gives this to Kosh: either he helps the Alliance to fight Shadows (and face an inevitable and lethal retribution for breaking the no-direct-confrontation agreement the two races had) or he would have to kill Sheridan, who firmly refused to take "No" for an answer (and was crucial to any victory over the Shadows). He chose the former.
This show loved this trope. It's revealed that the Minbari (or at least, some of them) knew of the Shadow invasion, and deliberately did not help the Narns when they were invaded by the Centauri with the help of the Shadows. But they held back because if they had moved to stop the Shadows, the Shadows would have started attacking openly sooner than they eventually did. As Delenn states in the episode "Ship of Tears", it was a choice between the lives of millions (on the Narn homeworld) and the lives of billions (on entire planets that could be destroyed by the Shadows, as they later proved capable of doing). The Minbari choice bought enough time for the Alliance to find a weakness of the Shadows...but only just enough.
And earlier, Sheridan (in the episode "In the Shadow of Z'Ha'Dum"), who was facing the decision of whether or not to release the dangerous Mr. Morden from the station's holding cells, made a reference to the attack on Coventry in World War II, repeating a rumor of the time that Churchill had deliberately allowed the attack to go through simply to keep their knowledge of the Enigma cipher secret (in actuality, action was likely taken, but went wrong; Straczynski admitted that the Coventry example wasn't a certain one, but it made for a good story and illustrated his point well). As one character comments in that same episode: "How many lives is a secret worth?" Sheridan lets him go, as to keep him would have revealed the "secret" and cost billions of lives, as the Minbari decision showed above.
Blood Ties: In the series finale, a demon makes Vicki choose between the life of one of her friends, or the power to save the world, which includes reversal of her near-blindness. She chooses her friend.
The serial killer Pelant starts draining Hodgins's massive fortune, using the exact same server that controlled the drone he was using to attack a school in the Middle East. The team is already tapped into the server and could easily shut it down, saving the money, but doing so would prevent them from stopping the drone before it could reach its target. Hodgins doesn't hesitate to choose his own poverty over allowing the children to die.
In the Eighth Season finale "The Secret In the Siege" after Booth accepted Brennan's marriage proposal, Pelant contacted Booth by cell phone, announcing that he would kill five innocent people if Booth didn't break the engagement. At the end of the Season 9 premiere, Brennan assured Booth that she has absolute faith in him (a major step for her given her mistrust of the concept of faith over the years) and will stand by him no matter what, saying only that the next time it will be Booth's turn to propose to her. Which he did at the end of "The Sense in The Sacrifice", after he finally killed Pelant.
Willow and Anya have made a powerful troll angry, and he tries to kill them both, and Xander jumps to their defense, but isn't not much of a match for the troll. The troll is however impressed with his bravery, and offers him to spare one of the girls, if Xander chooses which one of them he shall kill. Xander's response: "I'm not gonna choose between my best friend and my girlfriend! That's Insane Troll Logic!"
And in the season five finale, Buffy has to chose between her sister, or the whole of reality. She takes the third option - Heroic Sacrifice.
Charmed: Piper and Phoebe dealt with this when they had to either choose to save their sister Prue, or stop the bad guys...who in this case happened to be the Horsemen of the Apocalypse, meaning that saving Prue would trigger the end of the world. Piper was adamant about doing it anyway, then somehow saving the world after that. Only after seeing a vision of the future did Phoebe realize Prue had to be sacrificed to save everything else. Luckily, they Took a Third Option in the end.
Piper is forced to face another one of these in season five. Phoebe is kidnapped by a demon to use her body as a host for his lover's soul. Cole arranges for Paige to be taken as a host instead, which results in Phoebe being turned into a mummy and Paige being possessed. Cole then goes to Piper and tells her that she gets to choose which sister she gets back: if she chooses Paige, then Phoebe's body will be used as a host, and if she chooses Phoebe, the demon inside of Paige will set her free but keep Paige's body. Piper stresses over this seemingly impossible choice until she fakes choosing Phoebe, Takes a Third Option by removing the demon's spirit instead of Paige's from Paige's body, and relies on the spell knowledge Paige picks up from sharing the body in order to free Phoebe.
Not surprisingly, some Unsubs like to use this. An episode had the Unsub lock three friends in an underground chamber to deprive them of food and water. They are told that one of them has to die for them to survive. Even worse, they had to kill the unlucky third friend themselves. With a hammer.
Notably, Reid is forced into this twice in Revelations. In one instance, he is shown four computer screens of complete strangers and is told to pick one to live and one to die (logically, he's picking one to live and three to die - Reid brings this up almost immediately, though not in so many words). If he doesn't choose, they all die. Reid eventually gives in and arbitrarily picks a victim to live and is left to watch the others be murdered. Later, Rafael tells Reid to choose one of his colleagues to die. If he doesn't choose, Rafael will shoot Reid. He uses this to his advantage in one of the cleverest maneuvers Reid has ever made, which is saying something.
The Dead Zone: A variant occurs in one episode, in which the villain is fate. After some visions, Johnny is forced to choose which of his old friends die. Does he let one friend get a heart transplant at the cost of the other friend's life? He keeps trying to try the third option, but it never works out. Leads to some very Tear Jerker moments.
Doctor Who: A reoccuring them The Doctor has to face nearly once a season.
In the Series One finale "Parting of the Ways" The Doctor has to choose between using a cobbled-together weapon that can destroy the Daleks, but also everyone else on a future Earth or do nothing. He can't bring himself to do it and the Daleks bomb the Earth killing everyone anyway. The rest of the universe is only spared thanks to a last minute Deus ex Machina.
In the episode "Family of Blood", the titular family capture both the Doctor's companion, Martha, and his love (or at least John Smith's love), Joan, and then giving him the option of which one to kill first.
Son of Mine: Which one of them do you want us to kill? Maid or matron? Your friend, or your lover? Your choice.
The Fires of Pompeii counts as one of the hardest choices the Doctor was forced to take, as he had to choose between sacrificing Pompeii or let the villains ruin the world. Worse, it was a fixed point in time.
Later on in "Victory of the Daleks", the Doctor has to choose between destroying the last five Daleks or preventing Earth from being blown up by a Dalek bomb. There is no third option - the Doctor saves Earth and the Daleks escape after gloating about his weakness being his compassion.
Supreme Dalek: Then choose, Doctor. Destroy the Daleks or save the Earth.
In the Series 5 episode "Amy's Choice", the Dream Lord forces Amy to choose between her nice, reliable, dull boyfriend Rory and the dashing, unreliable, charismatic Doctor.
Amy ends up with the same choice at the end of "The Angels Take Manhattan" after Rory was stranded in the past by the last Weeping Angel. With the added twist that, if she chooses Rory, she would be forever parted from not only the Doctor, but the familiar life she knew in the early 21st century. Without hesitation, she chooses Rory again.
Farscape: The "Look at the Princess" trilogy revolves around Crichton being pressured into marrying an alien princess since he is the only one who can give her healthy children (a prerequisite for becoming empress.) To...encourage...John to make the right choice, the current empress invites Scorpius to the proceedings and tells John, "My daughter, or that abomination. Choose." Not much of a choice given that Scorpius would dissect John's brain and whatnot.
Niska captures Mal and Wash, and has Zoe choose between them. It's subverted when she chooses her husband without stopping to think, before he even finishes asking her to choose. Niska is so irritated at being interrupted in mid-taunt that he decides to be extra generous and throw in Mal's ear. The director's commentary points out that while sadistic, it's not much of a choice: Not only is choosing Wash the emotional choice, but the pragmatic one as well (since Mal has a greater chance of making his own escape, is more capable of resisting torture, and if the crew is unable to rescue the remainder, Wash's piloting skills in the getaway would be invaluable.)
Bounty hunter Jubal Early pulls the variant of the Sadistic Choice on Simon in "Objects in Space" — if Simon doesn't help him find River so that he can take her in for the bounty on her head, Early will go back to the engine room where he has Kaylee tied up and rape her. Sadistic element is taken down a notch by Early reminding him that if he goes along with helping to find River, there might be an opportunity down the line where Early slips up enough for Simon to take control.
This is because Early's goal is to control Simon, not to make him suffer. He is indifferent to suffering. He just wants this to go smoothly, and jam tomorrow works best for that kind of thing.
The concept is spoofed in one episode. The topic of "if you had to give up either food or sex" comes up. Immediately Ross says he'd give up food. Phoebe counters with "sex or dinosaurs." Ross's face falls, and he says "it's like Sophie's Choice!"
Joey, realizing choosing sex or food was hard, replied: "I want girls on bread!" A similar dialogue occurs in an earlier episode:
Chandler: Hey, Joe, I gotta ask. The girl from the Xerox place buck naked (holds up one hand), or, or a big tub of jam. (holds up the other hand)
Joey: Put your hands together.
In Fringe, Walter—who has become increasing less able to focus on the Greater Good if it means directly causing harm or suffering—is the one to realize that the only way to save two worlds is to shoot someone in the head. Made considerably worse by that 'someone' being the love of his son's life. Somewhat subverted in that he thinks she'll live thanks to all the drugs in her system.
In Game of Thrones, The Caligula King Joffrey learns of a song poking fun of the late King Robert, his father (or so he believes) and summons the singer to play the song in his throne room before giving him a choice of which body part will be cut off as punishment.
Joffrey: Tell me, which do you favor? Your fingers or your tongue?
Hawaii Five-0: In the season 2 finale of the remake, Frank Delano tells Chin Ho that he has targeted Kono and Chin Ho's wife Malia for death, and that he might have time to save one of them if he acts immediately. He goes after Malia and gets Adam Noshimuri to find Kono. Adam saves Kono from drowning, but Chin Ho is too late to save Malia from being fatally shot.
Series/House Of Anubis: Joy and Fabian are given a choice at the end of season 3 - the mask or their trapped friends. They chose their friends.
Kaizoku Sentai Gokaiger: Near the end, the insanely massive Zangyack invasion fleet, something that the previous 34 Super Sentai teams could only delay for a few years by sacrificing their powers, returns to Earth. The Gokaiger can either face the fleet by themselves, a task which is the next thing to suicide, or use the Greatest Treasure in the Universe to retroactively wipe Zangyack from the face of existence — at the cost of doing the same to every Super Sentai. They end up destroying the Treasure and resolving to face the impossible odds, because that's what Super Sentai members do.
Law & Order: Criminal Intent: A psychiatrist forces couples to choose to save themselves and kill their spouse or be killed and let their spouse live. He did this nine times and only an elderly couple choose the "altruistic" choice. Ironically the killer was inspired by the sadistic choice put to his father and grandparents during the Holocaust. Yes, he was called out on it, and no, he didn't get it ("I'm doing real science! It's documented and everything!").
Lois and Clark: In one episode, a mysterious couple kidnaps Jimmy and Clark's adoptive parents. They then tie Jimmy to a bomb in an undisclosed location, while doing the same with Clark's parents in another location. The bombs are set to go off at the same time. They give Superman a choice of saving his friend or his parents, as he only has enough time to find and disarm one bomb. Sipes decides to Take a Third Option and uses a beam splitter to fry both bombs with his laser vision from the sky. The kidnappers are not happy, as they are actually Kryptonians sent to test Kal-El's qualifications for leadership of their Lost Colony. Their goal was to force him to make a tough choice.
Mash: In one episode, B.J. is forced to choose between cutting a rope that a wounded soldier is using to climb up into the helicopter he's riding in, or let the helicopter be shot down. He chooses to cut the rope. This drives him into a deep funk, especially after he tries and fails to find out whether or not the guy made it out alive. Then the Army awards him the Bronze Star...
Happens in a few Medical Dramas where a woman is pregnant and must choose between her life or the life of her unborn child.
An episode of House has this with an expectant mother who was to allow Cuddy to adopt the baby. The woman chooses her life over the baby's, but both end up surviving and she decides to keep the baby for herself.
In Grey's Anatomy had a woman in her late forties who had breast cancer get pregnant after she had long given up trying to. She was to undergo chemotherapy, but found out she was pregnant. She initially chose to terminate the pregnancy so she could get treatment for the cancer, but ultimately decided to keep the baby, since she didn't expect to live long anyway (her mother also died of breast cancer at that age) and wanted to live the rest of her life to the fullest. If the she died, her husband would be there to raise the child.
In Scrubs, the mother was unconscious as the time, so her husband had to make the decision.
Mighty Morphin' Power Rangers: In the "Return of an Old Friend" two-parter, Goldar says that he'll free the teens' parents (who had been captured by Rita Repulsa prior...) if they give up their Power Coins to him. They comply, but naturally, Goldar doesn't hold up his end of the bargain.
Nash Bridges: Nash was given one of these in the first episode of the sixth (and final) season. The Villain of the Week managed to get the drop on Joe and Cassidy and take them hostage. He then has Nash chose between them while showing them chained up on internet camera. (The implication is that the one he doesn't choose will be left to die.) Nash choses Cassidy. But after the villain hangs up, Nash reveals it was because Joe would be easier to find because the graffiti behind him belongs to a particular street gang.
NCIS: In the opener of the episode "Requiem," Tony is presented with a difficult decision (although it wasn't forced on him by an enemy). Gibbs and the childhood best friend of his deceased daughter are in a car that goes off a dock. Tony dives in and pulls both of them out, but neither is breathing. He begins CPR on Gibbs, and then looks over at the young woman lying on the dock. He goes over to her, glances back to Gibbs, who still isn't breathing. Tony makes the agonizing decision to begin CPR on the girl, instead of continuing with Gibbs. It's a subtle moment, but an important one: it shows that Tony knows Gibbs well enough to know that Gibbs would not want to be saved at the cost of the young woman's life, and that the womanizing, goofy, often annoying NCIS agent is mature enough to make the hard choice. Fortunately for everyone involved, both Gibbs and the girl are saved.
Once Upon a Time: In one episode, Snow White drinks cursed water, and is told she'll never be able to have children because of it. Later, Prince Charming's mother is poisoned. To cure both Snow and Charming's mother, they all travel to Lake Nostos, which has water that will fix everything. Only problem is that the lake dried up, thanks to Charming's actions in a previous episode. All that's left is one snail shell worth of water, and only enough to cure one of the two. And the choice is up to Snow White. She chooses to save Charming's mother. But Charming's mother fakes drinking it, and instead gives it to Snow White.
Person of Interest: In "The Crossing", Shaw only has time to save Lionel Fusco or his son from being killed by HR. She chooses the latter. Fusco tells her that was the right choice, and then manages to save himself.
Prison Break: In season four, Michael is offered the choice of keeping Scylla out of the General's hands or rescuing Sara. The choice gets worse when Christina Rose then calls and offers Michael the choice of keeping Scylla out of her hands or rescuing Linc. The Sadistic Choice has a three way.
Psych: Used in the fourth season finale. Shawn is given a choice between saving Abigail (his girlfriend) or Juliet (the woman he's in love with). He originally chooses to save Juliet, as he doesn't know Abigail's whereabouts. When he solves the clue about Abigail, the team splits up to save them both.
Lassiter also ends up having to choose between obeying the procedures and laws he loves and rescuing Abigail, and rescuing his partner. He doesn't blink.
"Sex and Drugs" reveals that Drexel is fond of these. First, he put Charlie up to killing Bill O'Halloran in exchange for Nora Clayton's life...and revealing later that Charlie will never get out of the O'Halloran's house alive as a result. Then, when Miles went off to stop Charlie, Drexel puts Nora and Aaron Pittman in a pistol duel in retaliation. Aaron solves this problem by supposedly shooting himself in the chest, and when Drexel got close enough, Aaron killed him off, revealing that his metal canteen is covering his chest and is bullet-proof.
In "Nobody's Fault But Mine", Sergeant Will Strausser tries to force one on Rachel Matheson when he asks her which of her children she wants to die. Rachel Took a Third Option by completing the power amplifier and then stabbed Strausser when he tried to rape her.
Sherlock: In the episode A Scandal in Belgravia, Irene shows Sherlock an email she stole from a Ministry of Defense employee. Sherlock uses this, and Mycroft's earlier comment on the phone, to deduce that terrorists are about to put a bomb on a plane. The government knows about this but doesn't want to spook the terrorists into finding leaks in their organization, so they are forced to allow the event to take place. The Coventry Blitz is mentioned as an inspiration. However, the government decides to Take a Third Option by loading the plane with dead bodies and piloting it remotely. Unfortunately, Sherlock inadvertently foils the government's plan.
In the much darker Season 8, Lex, who wants to pay back Clark and Lana for his condition reveals that the suit Lana stole in an earlier episode (which was meant to heal Lex) absorbs Kryptonite radiation. He then offers the sadistic choice- let Lana absorb the fuel in a kryptonite bomb on the top of the Daily Planet building and never be able to come near Clark again, or walk away and let the bomb go off, taking half of Metropolis with it.
In Season 9, Amanda Waller shows Clark a TV screen depicting an agent holding a gun to Chloe's head and demands that he serve Checkmate or watch her die. The gunman makes the fatal mistake of talking, allowing Clark to hear him and figure out his location. Then, he simply speeds over to him and takes him out.
LX-13 does this in the Season 10 opening. Tying Lois Lane up in a field, he sets fire to the crops around her; he's already left a bomb in the ''Daily Planet' building. He then confronts Clark, asking him whether he'll let his girlfriend die, or sacrifice thousands of people in the streets of Metropolis. Clark saves them both.
Spooks: In one episode, Fiona and Danny have been taken hostage and Fiona has to choose between her husband Adam (a fellow spy) and her son, she has no choice but to lure Adam into the abductors' trap. Adam then has to choose which one will die. But before Adam gets to choose, Danny sacrifices himself.
"The Collaborator" is one episode with three examples of this trope in a single plot. It's two days before Kai Opaka's replacement (the spiritual leader of Bajor) is to be chosen and the front-runners are Vedek Bareil and Vedek Winn. Then a collaborator (a Bajoran that helped the Cardassians with the occupation of Bajor) accuses Vedek Bareil of having collaborated with the Cardassians in a massacre that killed 43 terrorists (including Opaka's son). The episode's plot is spent following Kira who has to gather evidence that will prove Bareil's innocence or guilt. The three examples of the trope are:
The obvious example: Bareil is Kira's lover and Winn forces her to take command of the investigation. The more evidence she gathers, the more it looks like Bareil is guilty. Eventually, she's forced to choose between protecting her lover and revealing the findings of her investigation to the Vedek Assembly which will destroy Bareil if revealed. She chooses to inform the assembly of her findings. However, when she contacts the assembly to present her findings, she learns Bareil's already spoken to the council so she doesn't need to go through with it. She made the choice, however.
The less obvious example: Bareil is the favourite for becoming Kai and was also Kai Opaka's first choice for the position. He is faced with the option of confessing to the collaboration which will destroy him, ensure he never becomes Kai and give the position of Kai to a ruthless, power-hungry woman, or he can exonerate himself and take the position of Kai. In the end, he chooses to take the blame for the massacre, withdraws from the running for Kai, leaving Winn to become the new Kai.
The twist: The reason Bareil took the blame is because the real collaborator was actually Kai Opaka herself. The Cardassians threatened the lives of 1200 innocent Bajorans if the 43 resistance fighters weren't handed over to Cardassian authorities. Opaka was forced to choose between the lives of 43 people (including her own son) or the lives 1200 people. She chose to sacrifice 43 lives to save 1200. Bareil knew the truth and chooses to take the blame both out of respect for Opaka and also to protect the sanctity of the position of Kai which cannot afford to be rocked by a scandal such as a Kai being a Cardassian collaborator.
In the DS9 episode "The Assignment", Chief O'Brien's wife Keiko was possessed by a malevolent alien mind. In a twisted I Have Your Wife version of this trope, the alien, speaking through Keiko, gave O'Brien the choice of sabotaging Deep Space Nine, or watching his wife die. He was able to find a Third Option at the last minute.
Wesley is due to be executed for a trivial crime. The orbiting "God" wants to hold Picard to his own rule about obeying the Prime Directive, which would apparently forbid rescuing Wesley. Picard chooses to "bend" the rules and the entity buys it.
Another early TNG episode, "Skin of Evil," (the one where an evil oil slick kills Tasha Yar) features this. The evil oil slick, Armus, takes control of Data's arm (which is holding a phaser) and tells Dr. Crusher that she gets to choose who gets shot. Dr. Crusher chooses herself, and the entity quickly becomes bored with this game because none of the Enterprise's crew are giving in to the creature's desire to be tormented for its entertainment.
Star Trek: The Original Series: In the episode "The Empath", Kirk was given the choice to choose either Spock or McCoy to go through torture. His captors informed him that McCoy would likely die if he went through with it and Spock would likely go insane if he went through with it. And interestingly enough, Kirk probably would have chosen himself to go through the torture again if McCoy hadn't knocked him out first.
"Latent Image": This trope turned Logic Bomb when The Doctor is forced to choose between saving Kim's life or Jetal's life after an accident. They have the same chance of survival, but he doesn't have time to treat them both. He instinctively picks the one he knows best, something not covered by his programming, and suffers a nervous collapse.
A somewhat undermined one happens in the pilot. Janeway is seemingly given the choice: use the Caretaker Array to go home, or destroy it and save the Ocampa (ignoring the use of a time bomb in that choice). Thing is, Tuvok had earlier stated that without the Caretaker, it would take several hours to activate, and with Kazon reinforcements on the way, keeping it for several hours given the state of their ship was looking less an option (and that's not counting the fact that the Array might have had other parts damaged, not just the self-destruct when the Kazon ship crashed into it). A better Sadistic Choice would have been Janeway agonizing over negotiating the Array as a bargaining chip to the Kazon, vs just blowing it up.
Supernatural: Loves hitting Sam and Dean (especiallyDean) with this, particularly during season 5. Either say yes to being meat suits for asshole archangels and condemn billions of people to death, or we'll torture you and your brother with either a) stage 4 stomach cancer, b) broken legs, c) missing lungs, d) watching your loved ones die/suffer/do the torturing, e) a good old-fashioned, super strength beatdown, etc. Whatever suits the mood, really.
Three Kingdoms: Zhou Yu, trying to conquer Jingzhou, presents Liu Bei with one of these during the Sun-Liu marriage arc. If Liu Bei accepted the proposal and went to Wu to be married to Sun Quan's sister, he'd become Zhou Yu's hostage to be ransomed for Jingzhou - or killed. If he refused the marriage proposal, he'd insult all of Wu and give Zhou Yu a legitimate reason to declare war on Jingzhou anyway. Although when Liu Bei elects to go, deciding his own life isn't as important as keeping what he and his generals had fought for, Zhuge Liang comes through with three schemes to help him survive and escape anyway, thereby taking a third option.
Torchwood: Children of Earth: The alien 456 demands 10% of the earth's children or they'll kill everyone. Captain Jack Harkness does eventually figure out how to stop them, but has only moments to choose between sacrificing his own grandson (whilst his daughter, the child's mother, watches) or letting the 456 take 10% of Earth's children.
Twin Peaks: In the second part of the second season, Agent Cooper is forced to play a game of chess with Windom Earle. Whenever Cooper loses a piece, Earle commits another murder.
Wizards of Waverly Place: Humorously subverted in "Wizards vs. Vampires: Tasty Bites". Jerry and Theresa consider the possibility that they might only be able to save either Alex or Harper from Juliet's vampire parents. By the time of the confrontation, however, they've already decided to save Harper - reasoning that she's the one who will take care of them in their old age.
It's at least very strongly implied that Mulder's father had to choose if his son or his daughter would be taken for experimentation.
In Season 8, Krycek gives Skinner a choice. He will give Skinner the antidote against the virus that is killing Mulder (recently returned from being abducted), but Skinner has to kill Scully's unborn child. In the end, he chooses to kill Mulder by unplugging his life support, which leads to the realization that the life support was only incubating the virus. A strong course of antivirals later, and both Mulder and baby are very much alive.