Near the end of Breath of Fire II, you're asked to sacrifice one of your party members in order to get the ultimate dragon power. It's a Secret Test of Character - you pass by refusing to sacrifice any of them.
It's supposed to be the one Eon feels the most for, since the weapon's power is equal to the feelings invested in it.
In Marvel Ultimate Alliance, the player is offered by Mephisto the choice between freeing Jean Grey or Nightcrawler from his realm. The one chosen is saved while the other is dropped into an energy vortex, and later his/her soul becomes brainwashed by Mephisto and aids him in the boss battle following the choice. S/he pulls a Heroic Sacrifice when you defeat the devil afterwards. Bonus points if you have the 360 DLC which includes, yes, Nightcrawler as a playable character.
There's even an easter egg in the epilogue scene, if the player saves Jean over Nightcrawler. Mystique becomes overcome with grief over her son's death and lashes out by assassinating Professor Xavier. There's a scene where the X-Men are attending Xavier's funeral, and one of them is f*** ing NIGHTCRAWLER!
And heaven forbid a player thinks intelligently and try to open both of the cages at once using UA's co-op mode. You will get both bad endings. Both characters "Survived", in that they whined in the safe house. But you will get both of their epilogues together.
If one has Magneto in their party when they have to make a choice, good ol' MaggyTakes a Third Option and uses his powers to break the locks on both cages. Choice averted. Players rejoice.
In 358/2 Days, Sa´x tells Axel he must choose which of his friends will survive - Roxas, or Xion. As one might expect, he does everything he can to Take a Third Option. It backfires, and he ends up losing both instead. Ouch.
Not so much a Sadistic Choice as being realistic: It turns out Xion's existence as an imperfect clone of sorts means she's leeching power from Roxas in order to survive. And the balance is unsustainable, which isn't helped by the fact that Axel has, well before this point, killed the guy who made her. Sa´x is being blunt - Axel can try to delay the inevitable, but at some point, Xion will end up draining Roxas to death if one of them doesn't get killed. Though, it still doesn't help that no one other than Axel actually cares if one of them dies. It's the fact that he makes an effort to bury the knowledge - which one of them finds, and which makes the other one realize how expendable they're being treated, that makes them both leave.
A minor variant in Super Smash Bros. Brawl, where Petey Piranha kidnaps both Princesses Peach and Zelda. Kirby (or rather, the player) can only save one princess; the other gets nabbed by Wario. This subverts heroic attempts to break them both out in that, while it is theoretically possible to deplete both cages' life bars by attacking Petey Piranha's head, the game picks a princess for you if this is the case. Nice try, hero. Both end up fine near the end anyways.
In The Legend of Zelda: Twilight Princess, before the events of the game, Zant gives Zelda the choice of surrendering to him or killing her along with all of Hyrule. Zelda decides to surrender.
Episode 1: You have to choose whether to save either Carley or Doug.
Episode 2: First, you have to choose between cutting off the teacher's leg or leaving him in the bear trap for the walkers. Second, when trapped in the meat locker, Larry has a heart attack and stops breathing. Since anyone who dies with an intact brain stem becomes a walker, you have the choice of holding back Lilly from trying to revive him so Kenny can crush Larry's head with a salt lick, or trying (unsuccessfully) to revive him. Another one comes just after that, when you have to choose whether or not to spare the St. John brothers.
Episode 3: Duck gets infected. You either kill him yourself or make Kenny, his father, do it. Later, you have to choose whether to help Omid or Christa onto the train first, but it's subverted since whoever you don't help catches up anyways.
Episode 4: Ben, who's been The Load for almost the entire season, falls off the balcony in Crawford's belltower. You have to either let him go, fufilling his Death Seeker mentalities, or save him.
Episode 5: When Lee gets infected, you have to choose whether or not to cut off his arm to slow the infection. At the end of the episode, you either let Clementine shoot you when you're about to succumb to the infection/blood loss, or just tell her to leave you for dead.
The trend continues into Season 2. The final choice of episode 1 involves risking saving either Pete or his nephew Nick. In a mild subversion, Nick will survive if you pick Pete, but his fate is currently unknown, and Pete has a wound which looks scarily like a walker bite.
In Vince's chapter of the 400 Days DLC, you're chained up to a rational and unapologeticwhite-collarCon Man, and a humanistic and remorseful rapist. Walkers surround the bus and a shotgun lands in your lap. You can escape with one of them, but it means blowing the foot off the other guy and leaving him to his fate. The question is, which one do you escape with and which one do you sacrifice?
In the PS2 game, Radiata Stories the major branching off point is whether or not the human hero joins the girl and the forces of non-humanity, or stays with humans. This results in two Multiple Endings, one where humanity survives but the girl dies; or humanity is replaced by elves and other creatures but the guy gets to be with the girl.
In the final episode of Desperate Housewives: The Game, your mobster ex-boyfriend gives you a gun and orders you to shoot either your husband or your other ex-boyfriend (long story). Whether you shoot your husband, ex-boyfriend or just take the very obvious third option and shoot the gangster, the end result is the same - the gun wasn't loaded, he was just testing you. That's almost as sadistic as the bad writing enforced on you the entire game.
In Mass Effect 1, during the attack on Virmire, you are given the choice between going to reinforce positions held by two of your officers: Lieutenant Kaidan Alenko and Gunnery Chief Ashley Williams. As the player is on a strict time limit to the detonation of a massive nuke, there is no time to Take a Third Option, and the one you do not choose to help will die. The choice is especially effective as due to the lead-up, you're given numerous occasions to reconsider. Massive indecision follows.
Then, shortly before the endgame, you are asked to chose whether to call the Systems Alliance ships into the battle in time to save the Destiny Ascension, the asari flagship which the Citadel Council is currently on board, or have the Alliance ships hold back and wait for the best opportunity to attack Sovereign. This one isn't quite as sadistic to the player, since Sovereign gets defeated either way, making it a choice between sacrificing either a lot of faceless Alliance soldiers or the Council and a lot of faceless asari. If you become a complete Renegade, you can decide to sacrifice the Council, then explicitly stateyou wanted them deadspecificallyto get rid of them so humans could become the new Council. Even Captain Anderson expresses utter shock, though Ambassador Udina is just fine and dandy with it. Utterly chilling.
In the Bring Down the Sky DLC, at the end the player must choose between letting the terrorist mastermind behind the attempted Colony Drop go free to save the hostages, knowing that he will probably kill more innocents later, or letting the hostages get killed in order to stop him permanently. Once again, there's no third option.
Letting Kasumi keep the Greybox in Mass Effect 2seems like an easy decision. After all, you and her went through hell to get it back, and its all she has left of her murdered boyfriend. Then you learn that the data the box contains would make the entire galaxy turn against humanity in less than a heartbeat if it ever got out.
In a sidequest in Mass Effect 2, you have two missiles being launched at a city and the spaceport next to the city. You only have the codes to stop one. Do you destroy the spaceport, cutting off the city from the outside world, or do you destroy the city, killing thousands of people in order to keep a valuable asset intact?
More accurately, without the spaceport the colony can't be maintained at all. It's explicitly stated that if you choose to save the city, the entire colony will have to be abandoned. This actually makes it a very interesting scenario because the stakes are so different in scale i.e. hundreds or thousands of civilians (the game is inconsistent about which one it is), against the entire colony (populous colonies can count millions of people).
Also in ME2, there are two separate instances in which Shepard must mediate an argument between a pair of squad members: Miranda and Jack in one instance, and Tali and Legion in the other. If Shepard hasn't accumulated enough Paragon or Renegade points to talk both sides down, s/he will be forced to chose to support one at the cost of the other's loyalty... which can lead to the death of the non-loyal squad member during the Suicide Mission.
And in Mass Effect 3, there are at least two Sadistic Choices in the main mission string alone. Both have third options, but they each require you to have made very specific choices in the past two games - and there is no way for fan-favorites Wrex and Mordin to both come out alive. For players without an import, the third option is not available and the other two options are indeed sadistic.
The ending of the third game also qualifies for most players. Shepard has to choose between destroying all synthetic life, taking control of the Reapers, or melding organic and synthetic life. The first involves murdering the geth (assuming the player didn't already do that) and a popular squad mate, does more harm to galactic infrastructure than the other endings, and leaves open the possibility of future wars between organics and synthetics; on the bright side, it's the only ending in which Shepard can survive. The second kills Shepard, and leaves open the possibility that the Reapers will someday break free and terrorize the galaxy again. The third is generally considered the "good" ending; it still kills Shepard, and subverts the free will of the affected species in a way that bothers many players, but it at least resolves the organic-synthetic conflict in a fairly durable way. There's also the Refuse ending: the Reapers eventually get defeated in a subsequent cycle, but the current harvest succeeds, every sentient being from the current cycle dies.
In Lost Magic, Diva of the Twilight holds her own sister Trista hostage for Issac's wand, which is one of the MacGuffins. And no, you don't get a third option. Due to the game's morals, Issac will turn evil and become Diva's subordinate if you decide to hold onto the wand.
Further spoilers ahoy: You still have the wand yourself. But on the evil path, you have to kill off the other sages. When you defeat the last one, if you choose to finish off said sage, you get the Bad Ending where Diva kills Issac. Even if you don't, you still will get a Downer Ending.
In the final case of Phoenix Wright Ace Attorney: Justice For All, after you learn that your client Matt Engarde was the one who ordered assassin Shelly de Killer to kill Juan Corrida, you are, towards the end of the final day of the case, forced to decide the verdict of the trial. Oh, and your sidekick Maya is being held hostage by de Killer, and the only way he will release her is if you get a Not Guilty verdict for Engarde. But if you do that, an innocent woman will almost assuredly be convicted in his place. The way to win is to Take a Third Option and convince de Killer over the phone to abandon his contract with Engarde, freeing Maya and letting you give Engarde his justly-deserved Guilty verdict. In the process, Engarde gets his own unpleasant choice—go free and get killed by de Killer, or plead guilty to murder.
Crowning Moment of FunnyandCrowning Moment Of Awesome at the same time if you convince the judge that Engarde is innocent after all of that plays out. Convincing de Killer to end his contract with Engarde involves proving to de Killer that Engarde was going to screw him over later on... in the courtroom. Nearly everyone in the room realizes the subtext of what Phoenix and de Killer are talking about, and de Killer pretty openly promises to kill Engarde for it the moment Engarde is alone, while also informing the police of his (hostage's) location. If you convince the judge that it's best for Engarde to go free after this, Engarde freaks out and demands to be put in jail.Very satisfying.
Grand Theft Auto IV gives you a choice of two paths at the end of the game: You can either choose to participate in a mission with Dimitri, the Russian crook who screwed you over earlier in the game and who you've been trying to kill up to this point, or not participate in the mission and instead, to go and kill Dimitri. If you choose to kill Dimitri, the mob boss who set up the mission for the both of you will show up at Roman's wedding and kill Niko's love interest, Kate. If you choose to do the mission, Dimitri will show up at the wedding and kill Niko's cousin and best friend, Roman. Ironically, it was Kate who advised you to go kill Dimitri, while it was Roman who advised you to participate on the mission with him.
Fable II ends with you having to make one of three choices: use the power of the Spire to resurrect everyone in your family Lucien killed — your husband/wife, your kids, your dog, even your long-dead sister comes back for a while — or use it to resurrect the thousands that Lucien killed to power up the Spire. Or you can choose to take 1,000,000 gold, but that's both a major dick move and outside the bounds of this trope. It's not quite a Sadistic Choice, as under normal circumstances all of these people would stay dead, but still a good source of angst if you're looking for one.
The money one is useless, except for the achievement and seeing all the endings (at this point, one should have an amble supply of money). The best choice is "Love", as that is the middle one and more importantly, allows one to retain the dog which is useful for finishing the Archaeologist quest (which, if one is doing, should mean something as even if you know exactly where everything is, it is still time consuming). The sadistic choice is the one with the Shadow Court, where you have to choose to curse yourself or an innocent girl. While it has little effect on the game, it would be a rather difficult choice in real life (although, in real life, rapidly aging oneself when one is the only one who can save the world would be foolish).
When you must sacrifice either yourself or a young woman you've never met to a fate of losing all of your youth and gaining glowing red eyes.
Fable III gives you one in the first scene: After asking your older brother, King Logan, to spare the protesting peasants, he punishes you by letting you choose whether he executes your childhood sweetheart or the leaders of the peasants. What's that? You want a third option? Sure. You can choose to do nothing, and Logan kills all of them.
In the Heaven's Feel arc of Fate/Stay Night, you have to choose between stopping Tohsaka to save the one you love, Sakura, who will inevitably go on a killing rampage, or killing said love and upholding your borrowed ideal.
Regrettably, choosing to kill her only leads to a bad end - right after getting told that what would happen next was probably enough for it's own route.
Fire Emblem Shadow Dragon for the DS (Marth's game) in one of the early chapters the player has to choose one character to stay behind as decoy, thereby losing the character
The effect is completely lost on the players that sacrifice Jeigan or Gordin (both are considered completely worthless)
Fire Emblem Radiant Dawn has a rather gripping one near the end of Part 3. Just as Micaiah is about to give the order to fire on the Apostle, Tibarn swoops in and hangs her Bodyguard Crush Sothe over a cliff and gives her an ultimatum: cease fire and retreat or Sothe dies. Micaiah can't retreat however, since it would effectively mean everybody in Daein would die due to the bloodpact. Unable to find a third option, Michiah is helpless as she watches Sothe get thrown over the cliff. Micaiah promptly has a My God, What Have I Done?, until it is revealed to have been a bluff and she calls for a retreat.
Fire Emblem Awakening has one in Chapter 9. Chrom must choose between giving King Gangrel the Fire Emblem, or allowing him to execute Chrom's sister, Emmeryn. However, the choice turns out to be irrelevant; either way, Emmeryn will sacrifice herself via willingly throwing herself off the cliff she was supposed to be pushed from by Gangrel, allowing Chrom a chance to escape with the Fire Emblem in hand.
This seems to be a theme in the game, as there are several times where you have to decide one thing or the other, but it usually doesn't have any impact on the story with what you choose, with something else conveniently choosing for you.
In the Final Battle, Naga presents a choice: if Chrom strikes the final blow to Grima, the Fallen Dragon will be resealed but will eventually be waken up in a millenia. If the Avatar does it, he/she and Grima will be destroyed forever because the Avatar and Grima are technically one and the same. The Avatar does ultimately survive in the end, but nobody knows that will be the case when the decision is made.
A slightly different spin on this occurs in Call of Duty: World at War during the Soviet campaign level Eviction. After being ordered to kill wounded Germans crawling on the ground in the streets of Berlin, you and your squadmates stumble upon three unarmed German soldiers cornered in a subway entrance. Your Sergeant gives you the choice of gunning them down yourself or letting your vengeful Red Army comrades throw Molotovs at them.
Later in that same game, a more traditional Sadistic Choice occurs when Sergeant Roebuck and Private Polonsky are attacked by a trio of Japanese soldiers pretending to surrender. It's impossible to save both as shooting one set of soldiers attacking one member of the duo causes the other group to succeed in their suicidal attack on the other. This causes the surviving NPC to go on a Roaring Rampage of Revenge when the time comes to Hold the Line.
Call of Duty: Black Ops 2 offers another one in Farid's playable segment, which ends with the choice to either shoot Mike Harper to maintain his cover, or try to take out the Big Bad Menendez right there. Shoot Harper and you obviously lose him for the rest of the game, and Farid is visibly shaken by the experience. Try to shoot Menendez, though, and things are even worse - not only does your attempt to kill him fail, but now Chloe Lynch, whose survival is necessary for the Golden Ending, will also die in the next mission, since Farid will not be there to protect her.
In FAMOUS: Kessler pulls this on Cole. Cole is given the choice to save six doctors, or save Trish, his girlfriend. The doctors are more relevant in context, because the setting is a city under quarantine due to disease, and the quarantine has been causing basic social services to fail while gang violence escalates to the point of insanity. If Cole goes for the doctors, Trish dies. But there is a twist if you go for Trish instead; the choice is rigged and Trish will be a decoy, with the real Trish hidden with the doctors Cole has chosen not to save. Notable for two reasons: First, the hero doesn't get to Take a Third Option, and second, it's actually a subversion. Kessler isn't doing it because he's a sadist, he's doing it because his ultimate goal is to harden Cole against emotional trauma earlier in his life than he would be otherwise.
It comes up again in the sequel: In the end, you have the choice to either defeat the Beast and in the process kill all Conduits, including Cole, Nix, and Kuo... or side with the Beast to save the Conduits at the expense of Humanity, including your friend Zeke. And no, there's still no Third Option — you either wipe out humanity to save yourself and those like you while turning your back on your human friends, or sacrifice yourself and some of your closest companions to save humanity. And yes, they areKilled Off for Real, with the possible exception of Cole in the Good Ending.
The main plot of Wild ARMs 1 is kicked off by one of these. The heroes have to either give the demons the Tear Drop, or allow the demons to destroy Adelhyde. They're forced to do the former.
In Quest for Glory V, the hero will venture into Hades at one point. At the end of the level, he'll be given the choice to resurrect someone implied to be closest to his heart: Katrina, the vampire who died for him, or Erana, whom he forged a spiritual bond with. Both women are in love with him and he can only bring one of them back to life.
You can choose to save neither, but that doesn't really count, does it?
Sith in Knights of the Old Republic are fond of this. One of them would torture your Love Interest Bastila (if you play male) or Carth (if you play female) to extract vital information from you. Another one subjects you and one other guy to a sick game: if you answer some questions wrong, he Force-electrocutes you, but if you answer right, he Force-electrocutes the other guy! In the latter case, it's only this trope from point of view of a heroic Player Character, as the whole point is that a true Sith, which he thinks you're aspiring to be, would always make the sadistic-towards-someone-else choice. One of the ways out is to Take a Third Option and team up with the other guy to kill your tormentor.
Far Cry 2 contains such a scenario, the player character receives word that one of the factions in the civil war plans to wipe out a bunch of uncooperative civilians and his fellow foreign mercenary friends, and only has enough time to get to one to assist in defending. Ultimately though it doesn't matter which option one chooses, the outcome is the same either way.
Silent Hill 3 has a sadistic choice that the Word of God has admitted to have been purposely worded that way to make the player uncomfortable. A woman of the Order confesses to Heather and begs for forgiveness. Remaining silent makes you feel like you did something wrong, but forgiving the woman gives you a tremendous number of Dark Points (and is what most people do in order to gain the Bad ending).
Silent Hill: Homecoming offers a different variation of the sadistic choice; at one point in time, you are given the option of watching your mother die by being torn apart on a torture device, or shooting her yourself so she won't have to suffer. Neither choice is particularly pleasant.
Ace Combat X: Skies of Deception offers you something of this in the endgame. You can either take down Alect Squadron first, which leads to the Fenrirs having annoying High Powered Microwave cannons, or you can attack the transport fleet first and deny the Fenrirs their HPMs, but gain Alect Squadron's piloting expertise. And you may also need to go through an Airstrike Impossible segment now or later. No third option here, folks.
In the City Elf origin, you can kill the noble who's about to rape four elven women, but that would bring down the wrath of his father, who would purge the Alienage—so it's either let him get away with raping (and possibly killing) four women to save your town, or killing him and forfeiting your township down the line.
The chronologically first (for most characters) major Sadistic Choice in Origins takes place in Redcliffe: the Arl's young son is possessed by a demon, and the only immediate options available to the party are to fight the demon in the physical world, killing the boy in the process, or perform a blood magic ritual wherein his mother gives her life to allow one of your mages to confront the demon in the Spirit World. You can Take a Third Option, instead, but it requires you either to have already saved the Circle mages, or to go save them first and come back with their help. If you do, the epilogue reveals that the boy never exactly went back to normal, and Wynne mentions that a mage cured this way will be forever changed by the experience.
Another, somewhat more surprising one is deciding the fate of Teyrn Loghain, who was really a Well-Intentioned Extremist and ultimately seems to recognize and regret his errors. If you choose to spare him and give him a chance at redemption, one of your party members abandons you and becomes a hopeless drunk for the rest of his life—assuming the guy you just spared doesn't have him executed, which is also a possibility. Again, you can Take a Third Option and harden his personality beforehand, Alistair can be crowned king but will remain forever bitter and despondent over either how Loghain almost walks away scott free or how he gets to play hero. Interestingly, the default option for the first game's ending in Dragon Age II is actually the third option, as you get to meet King Alistair who grimly mentions that Loghain is still alive.
And then there's the end game, where you have four options on how to kill the Archdemon: perform a Heroic Sacrifice which not only kills you but destroys your soul, have your Grey Warden brother-in-arms (an possibly love interest) Alistair perform the soul-destroying Heroic Sacrifice, let Teyrn Loghain do it (only available if you spared his life earlier, see above, but quite possibly the most ethically unproblematic decision), or help your Sour Supporter Morrigan give birth to what may be the equivalent of the Big Bad. If you decide to take up Morrigan's suggestion, one of the male Grey Warden party members obviously has to help her conceive the baby. This isn't that big of a deal, unless your player character is in a relationship with Alistair, because if you take that route, he will end up being the only guy in the party capable of playing baby daddy... and if you don't, he will go and sacrifice his own life for you in the end, regardless of what else you have to say!
And then the expansion, Awakening ups the ante by forcing you to choose between saving the city of Amaranthine (a major population center) or the Vigil's Keep (where your soldiers and half your party are stationed) from getting sacked by the Darkspawn. Thankfully, you can Take a Third Option again: if you have invested heavily into reinforcing the fortress and its troops, the Vigil's Keep will manage to fend for itself while you defend Amaranthine. While the Keep's losses will still be significant, none of your party members will die if you maxed out its defenses.
Dragon Age II, however, shows no mercy in its sadistic choice, when Anders destroys the Kirkwall Chantry, Hawke is forced to choose between the Templars and the Mages and with it, potentially half of the party who have their own reservations about the freedom of mages. Despite taking a side, Hawke ultimately has to fight the leaders of both the Mages and Templars. For Hawke who sided with the Mages, Orsino was partially responsible for his mother's death while if Hawke sided with the Templars, Meredith has clearly gone insane.
In the 2005 version of The Bard's Tale, you get a choice between saving the princess you've been trying to save, and killing her at her kidnapper's request (who insists she's a demon). If you choose to kill her, she turns into a demon. If you choose to kill the wizard, you beat him and THEN she transforms into a demon, who keeps you as her right-hand man.
You also have a third option, to ignore both of them, go back to the bar you started at, and just get used to the undead horde that's been rising to conquer the world. They're not that bad.
Yume Miru Kusuri presents you with three girls, you can only save one from their painful problems. Once selected, your character watches the other two their slow inevitable and painful descent to despair from their problems while you are merely buying extra time for your selected girl. She too can join the others in a bad ending if you made the wrong choices
Legend of Mana: Near the end of the Heaven's Gate arc, Escad and Daena come to blows. You get to decide who to side with, causing the other person to initiate a battle to the death. You can't even Take a Third Option, as saying that they're both wrong causes the one you've been nicer to to flip out and try to kill you.
Many, many instances in The Witcher. An early example has Geralt having to decide whether or not he should give a crate of supplies he just defended to a desperate band of travelers. If he gives them the supplies, he later discovers that the "travelers" were actually terrorists, and the "supplies" were weapons they used to murder an innocent man. If, on the other hand, Geralt sees through the terrorists' lie and kills them, he later finds out that his actions caused the arrest of an innocent man. Either way, someone gets screwed over.
The sequel is likewise full of this. A major example is the climax of chapter 1, where Geralt must choose between helping Iorveth save a group of elves about to be executed by Loredo, or help Rosch go straight after Loredo and kill him. You cannot do both. Choosing to help Iorveth causes Loredo to escape, spark a mass race riot in Flotsam, and completely get away with it. Choosing to help Rosch kill Loredo results in the elven hostages dying, but the riot, and thus more bloodshed, is prevented.
Fallout 3 DLC The Pitt. You can either defeat the slavers and kidnap the leader's child. This means that the Pitt loses its standing army, the child is subjected to rough treatment and the freed slaves may not even able to discover the cure to the massively degenerative disease them as none of them seem to have scientific knowledge. On the other hand you can crush the slave rebellion, allowing an army of slavers and raiders to terrorize the region and slavery continues in the Pitt, probably even after a cure is found. Don't rely on the Karma meter to tell you which is right, those popups won't give you any comfort now. Worst of all, even after you make yourself believe you did the right thing you then remember that those subhuman creatures the disease turns them into were the only large scale food source available in the Pitt.
In Point Lookout, regardless of whether you side with Desmond or Calvert, the latter always turns hostile at the end.
In Super Robot Wars Original Generation (and possibly the Alpha series as well?), Elzam's backstory centers around one of these. He can either let a space colony be exposed to nerve gas while he chases the villain, or blast open a hole and launch both the canister and his wife into space. His wife was already exposed to the gas anyway, he just couldn't pull the trigger himself until she begged him to.
In the Fan Remake of King's Quest II, there is a flash-forward to the era of King's Quest III. Daventry in ruins from the ravages of a three headed dragon. Graham's son was kidnapped as an infant, and Graham's daughter has given herself up to sacrifice to try and appease the dragon, knowing it's only temporary. And then the The Father, the Chessmaster who set all this crap up in the first place, shows up to gloat. He then presents the choice: if Graham give up the crown, the Father will remove the curse he's put on the family, dismiss the dragon, and restore Daventry. He will even give Graham his children back. The full points option (it's playable) is telling him to rot in hell.
The first Another Century's Episode game features one of these: Either blow up civilian space shuttles at random trying to locate a bomb, or let that bomb get to Earth and completely wreck the environment.Thanks a bunch,, Char.
Prince of Persia (2008) ends with a pretty hefty one for the Prince: Elika, the Prince's Love Interest, has just died to re-sealAhriman, so the Prince has the choice of either letting her stay dead, or using the power of Ahriman's prison temple to resurrect her, thereby releasing Ahriman and resetting everything he's done. It really tells you something about his character when he brings Elika back. She's not happy about it.
A justification in the Epilogue: The Prince (rightly) states that all that had been accomplished was putting the Sealed Evil in a Canback in its can rather than actually destroying it, meaning that at some point in the future, this whole process would start all over again... except this time without the one thing that could stop it from winning: Elika. So reviving Elika (although an emotionally-driven decision) actually does have some logic to it. Let the world live on for another few hundred years before almost certainly being taken over by darkness and evil and people who kick puppies, or take this one freak chance that has arisen due to circumstances that will likely never happen again to destroy the Sealed Evil in a Can forever? In the long run, the Prince's decision is the smarter one. You know, if what you're going for is keeping the world safe from this particular evil for the rest of time.
Final Fantasy VI has Kefka, of all people, invoking this on Edgar Figaro. He has his soldiers torch Figaro Castle and state that they'll stop torching his kingdom if he hands over Terra Branford. This backfires on Kefka when not only does Figaro escape with Locke and Terra, but he also orders his guards to have Figaro Castle tunnel underground.
The members of Garrosh's Horde who don't like his actions have this. Either go along with him and risk their people in what they see as a self-destructive and immoral war with the Alliance, or turn on him and suffer his wrath.
In Metal Gear Solid: Peace Walker, Hot Coldman, in a manner similar to The Joker's "Social Experiment" from The Dark Knight, managed to leak Peace Walker's false data to NORAD with the intention of forcing the military to choose between launching nukes, namely with the belief that humans don't possess the will to launch nukes, although he also hints that he truly doesn't care if they did launch in either case.
There may be a trend here: like Far Cry 2 and inFAMOUS, Alpha Protocol forces you to choose between the life of someone you care about, and the lives of many people you don't know. And just like them, the character you care about exits the story either way (though for once, she has a chance of not exiting in a body bag.) Interestingly in Rome, the choice is even more difficult. While the utilitarian decesion is to save the greater number of people, saving just Madison hurts the greater objectives of Halbeck further as she survives to campaign against them politically whereas if she dies the anti-terror laws, that were the motive of the attack, are passed.
Alpha Protocol has another example in the Taipei missions: Thorton has to stop Omen Deng from assassinating Taiwanese President Ronald Sung or at least he thinks Omen Deng is the assassin and at one point, he manages to recover Omen Deng's flash drive. The problem? The flash drive has protection software that deletes the disk when opened, so Thorton has to choose to either save the data about the assassination, or save the data about deliberately instigated riots planned to happen in the future. If he saves the data about the assassination, President Ronald Sung's life is saved but hundreds of people get killed in the ensuing riots. If he saves the data about the riots, the president puts extra security around to stop the riots before they happen, but the assassin successfully kills Sung.
In Team Fortress 2 you can invoke this on any inexperienced Engineer. When you sap his sentry you have to force him to either fix it, resulting in you being able to get away and possibly sapping again, or try and kill you and risk loosing his sentry. Most inexperienced Engies do not realise that the spy can instantaneously place a second Sapper as soon as the first one is removed, and those that do are often not nimble enough to catch experienced spies, who often lure them away long enough so that the sapper destroys the sentry.
Similarly, any person who plays Medic will at some point come across a situation where two or more people run up to them while burning or bleeding to death with neither dispenser nor health kit in sight. Your healing beam can only focus on one patient at a time. Occasionally the victims will have enough health that a particularly fast and skilled Medic will be able to bounce just enough healing to each patient for all of them to survive, but this is rarely the case.
None of the endings in Deus Ex are exactly happy but a better example occurs when JC is holed up with his injured brother. Government agents arrive and you can either go out through the door to fight them or slip out the window and leave Paul to his fate. The choice is more difficult if you have specialized your character for stealth.
This becomes almost a non choice if you know that you get captured when you're "killed" (which will happen inevitably regardless of choice) and that the only thing that truly chooses whether Paul lives or dies is if you exit the room via the door or escape out the window, respectively.
The ending of Killer7 presents players with one: kill Matsuoka, and the US will wipe Japan off the face of the earth; spare him, and Japan will attack the US, starting World War III.
In the last level of De Blob 2, the Big Bad has placed bombs around his enslaved workers and only Blob can save them. He taunts you to either waste time saving a few and let him get away with brainwashing the rest of the planet, or go after him and leave those few to die. But there's enough time in the level that if you're any good at the game, you'll be able to do both.
Although this is put in a rather subtle way, in BlazBlue this occurs to Litchi Faye-Ling. Hazama invites her to join the NOL because he has the cure for herself and Arakune. Her condition is worsening and if left be, she'll be at best a burden to Orient Town, at worst turn into the next Arakune and eat her former friends. If she just refused, there will be a big chance that Hazama will dispose the cure and her only lead for salvation lost. It boils down to either "Go betray those who expect you to be a good person and join The Dark Side" or "Slowly wither and die, or if lucky, turn into a monster that eats everyone who looks up to you." There's just no third option for her. She did have a third option: give up on Arakune and get Kokonoe to help her deal with her Boundary corruption which Arakune himself begs her to do in his true ending. She just refuses to take it because giving up on Arakune would have made all of her efforts pointless.
The end of Assassin's Creed III forces Desmond Miles to make a choice between letting the Earth burn in the hope of building a better civilization After the End, knowing that evil will eventually return; or saving the world but handing it over to a vengeful Physical God who will enslave mankind. The latter choice also comes at the cost of his life. He chooses to save the world, hoping that his friends will be able to stop Juno in the next game. To highlight how sadistic this choice is, Minerva actually recommends doing the opposite of what Desmond chose. In her opinion, setting Juno loose would be worse for humanity than a solar flare frying the planet.
A sadistic choice plays a pivotal role in the backstory of Arcanum: one of the dwarf clans carelessly allowed humans access to their secrets of technology, humans used that technology to destructive ends, and a delegation of elves petitioned the dwarf king Loghaire Thunderstone to allow them retribution against the clan (elves, being In Harmony with Nature, suffered most from the industrial revolution). To allow elves to interfere in the dwarven justice system would violate the clan's honor, but upsetting the elves could have led to a war which would have devastated the continent. Loghaire eventually gave in to the elves' demands, but was so ashamed of his decision that he abdicated the throne and exiled himself from his people.
In the penultimate story mission of Saints Row The Third: The player is forced to choose between going to Magarac Island to save some friends that STAG had kidnapped and strapped explosives to, but in doing so allow Killbane to escape; or go after Killbane and kill him, but in doing so allow your homies to die.
Mocked in Saints Row IV in the first mission, where you must choose one of two world-changing bills as a short button pressing event—a bill to support a cure for cancer ("Fuck Cancer") or a bill to end world hunger ("Let Them Eat Cake"). In a later mission, Zinyak offers you a choice to either continue your quest to rescue Matt Miller/oppose the Zin Empire (and face further opposition from the Zin) or give yourself up and ensure the safety of what's left of the human race (and get a Nonstandard Game Over where you're bluntly told "ZINYAK LIED").
For the final mission in The Bureau: XCOM Declassified, you get to pick a new Player Character from among Faulk, Weaver, and Weir. After you reach your assigned objective, both of the others get in trouble and ask for your help. You can only pick one, resulting in the other one dying. You also get another choice on whether to execute Carter or not. If you choose the second option, he will swear vengeance.
One of the early bosses in Demonicon is a cannibal who kidnapped a bunch of local refugees. Problem is, he happens to have blood-bound them all to himself, so if you kill him they die too, but if you let him go he gets to find a bunch of new victims someplace else. Unfortunately for good-aligned players, there is no third option to just let the prisoners go and turn him into a Sealed Evil in a Can or something.
In the backstory to Hatoful Boyfriend, the mother to Yuuya and Sakuya ran away with a commoner and had one chick and one egg before her fiancee had him murdered. Yuuya remembers her telling him about his "new father" and saying "But your new father says he doesn't want your brother. He says he can only feed you if you leave the egg behind." The phrasing suggests that she was only allowed to keep one of her children and elected that it be the one who had hatched already. To spare her Yuuya volunteered to throw his brother away, but kept the egg and switched it with the new one she laid, smashing the new one. Killing his unborn half brother as a child had a profound effect on Yuuya - he's not sure if he did it for his full brother or out of spite, just like the nobleman, and it haunts him. Either way, he would have had to kill his sibling or let his mother kill her son.
DanganRonpa and its sequel hinge on this: are you willing to kill all of your companions in order to escape?
Both of those games have an even nastier choice in the finale. In the first game, the final trial has the survivors choosing between Hope and Despair. Choose Despair? They surrender and stay in the school forever. Oh, and Hope, aka Naegi, gets executed. Choose Hope? The Mastermind dies, but they will be forced out of the school and into the outside world... which is a wasteland.
The second game has three choices. The survivors can either stay on the Jabberwock Islands with the members of the Future Foundation (AKA the "World Destroyers", which they are NOT; they're on the students' side), escape the Jabberwock Islands as intended, which will allow the Mastermind to escape too, or they can Take a Third Option and escape the Islands and slay the Mastermind... but run a heavy risk of going completely insane in the process.
Returns with a vengeance in Shin Megami Tensei IV. Issachar, already dying from wounds you inflicted on him, begs you to hurry and killhim. Much later, in the Chaos Ending's Playable Epilogue, a Mikado woman is surrounded by a flock of Halphas, and is offered either remain a human and be devoured, or just take a Red and become a demon.