Cruelty Is the Only Option aka: Plot Aided Bastardry
You know immediately that you are engaged in something like evil, if not evil itself, but our appetites as players demand that we seek objectives and conquer them - and the game scourges us for this dereliction of conscience.
When the player is forced to do something that seems unnecessarily mean in order to continue playing. This isn't just when you kill an enemy that's trying to kill you. That can be seen as self-defense. This is when you take an NPC who is a minor inconvenience to you or not in the way at all and have to intentionally harm, inconvenience, or psychologically damage that person.
Very often the reward gained for doing this seems disproportionately small compared to the damage the player caused.
Please note that this is when the player is forced to do these things. If the Player Character does it in a cutscene, then it doesn't count.
May lead to You Bastard, but often doesn't. Stupidity Is the Only Option is when the player is forced to violate their common sense in order to continue with the game. If both options result in some sort of cruelty, you have a Sadistic Choice.
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In Trio the Punch, the last level has you beating up a bunch of innocent animals. The game calls you out for this "CRUETY" (sic).
At the very least, the Bonus Boss you face after collecting all 50 Red Crystals admits that he was the one who started the slave-trade in the first place, which makes killing him that much more satisfying and helps balance the karma scales a little.
The Binding of Isaac follows the classic format of "kill all the enemies in the room to open the doors". One enemy in the game does nothing but run away from you while crying uncontrollably - you can't be hurt by them even if you try. You still have to cry at them until their heads explode if you want to make progress. On the other hand, their heads are apparently stuffed full of flies or sometimes bombs, so maybe it's more of a mercy-killing.
Messiah forces you to do terrible stuff sometimes — one example is filling the waste container (necessary to proceed); the only way to do so is by... dropping harmless scientists into a meat grinder. Another example is filling an entire complex with deadly radiation. Even Satan calls you out on this one.
If you decline her love, she will want to be alone, and any time you talk to her afterwards, she seems depressed.
You can return her affections, implying that you are breaking up with Zelda. However, she knows how important your quest is and decides to remain professional when interacting with you.
Grim Fandango has many examples of this. Manny does many excessively mean things to Glottis, including turning on a machine while he's working on it so it'll toss him around while he cries in protest, poisoning him to force him to vomit, getting him fired, etc. Another puzzle has him gunk up the company mail system, forcing repairs.
Glottis will at least protest being used as ballast to unbalance a tree marrow pump (long story).
At one point Manny locks up Raoul the claustrophobic waiter inside a closet, where the poor guy accidentally knocks himself out in a fit of panic. Notably, when Manny is locked up in a room later in the game, he finds the situation uncomfortable enough to feel sorry for that particular misdeed.
The Longest Journey: There are other things too, but special mention goes to Detective Minelli. First you poison him to get him to move, then you steal his glass eye (he obviously becomes very panicked when you do this). Other solutions involve conning your way around problems.
Police Quest 3 has an example of this. Eventually, you will meet a jolly janitor who had just finished cleaning up the bathrooms. Cue Sonny clogging up a toilet with a whole roll of toilet paper, sending the janitor rushing off to fight against the flood to follow soon after just so Sonny can unlock his partner's locker in the women's bathrooms.
In Monkey Island 2: LeChuck's Revenge, you have to trap Stan the salesman in a coffin and nail it shut to advance. In the next game, you find him still stuck in that coffin in a tomb on Blood Island, and finally let him out.
This got to the point where the developers cut out a scene in the game that would have had Wally accidentally drown trying to get his monocle after he dropped in the water. They couldn't do anything more to him without feeling bad.
In the third game, you find out that Wally has become a pirate after attending a seminar and listening to books-on-parrot. How do you get out? You make him cry. He feels better afterwards, though.
In Floyd, you need access to a phonebooth to change your clothes but a girl is talking to her boyfriend there. To advance, you need to spike his drink so he completely blunders and offends her. Since the world of Floyd is a horrible Big Brother dystopia, the girl promptly gets executed for being unhappy in public.
The Gabriel Knight series is pretty bad about this, although Gabriel is supposed to be kind of a jerk. Practically all the puzzles require lying, stealing, or otherwise manipulating people. In the first game, he repeatedly takes advantage of the generosity of his detective friend, Mosely, and at one point steals his badge and impersonates him just so that he can flirt with an attractive woman.
The Sam and Max games feature this constantly. For example, in "Abe Lincoln Must Die!", they trick one of the Soda Poppers into getting drunk on Bosco's "truth serum" so he'll provoke a war in the Dakotas. Of course, since Sam and Max are themselves moderately sadistic, this is completely in character.
Then in "What's New, Beelzebub?", they have to get Jimmy Two-Teeth's dying son sent to Hell by swapping his sin record with Jimmy's.
The Dig had a puzzle where you had to resurrect an alien turtle...thing with an explosive inside of it, in order to blow up another animal, once it ate it. It doesn't help that failing to resurrect the turtle properly causes it to come to life briefly and then melt away.
Every Broken Sword game has a section where you must rip off a Recurring Extra. For example, conning them out of $50 in the first game and getting them arrested in a 3rd world country in the second.
Ahh, the infamous Limbo of the Lost. Although at the very beginning of the game your character refuses to open a coffin, not wanting to desecrate the dead, he then goes on to steal a man's arm, remove copious amounts of bone from rotting corpses and skeletons, put a bear trap onto the eyes of one of the only sympathetic NPCs and hang a sleeping man so that you can access a control panel that he's lying on. And we're not even halfway through the game yet!
Strong Bad's Cool Game for Attractive People features a Jerk Ass main character, so naturally a lot of this occurs. The first episode alone has Strong Bad stealing Homestar's clothes and forcing him to run home naked, causing a fire in Marzipan's backyard, impersonating (and further humiliating) Homestar, breaking into the King of Town's castle, dropping the King of Town down a pit, flagrantly cheating in order to win the Tri-Annual Race to the End of the Race, framing Pom-Pom for taking banned supplements, and then tricking everyone at Homestar's victory party into falling out a window.
In the final case of Phoenix Wright: Ace Attorney: Justice For All, you're forced to accuse someone who you know is innocent (not to mention more than a little Woobie-ish by that point) to buy time. And to make matters worse, you also know by this point that you're defending an obviously guilty villain. The crowd even boos you for it. Almost guaranteed to make you feel like a terrible person.
You will torture more than a few rats in Ghost Trick. Various puzzles involve flinging rats across the room, dropping rats from the ceiling, spinning rats around and around, and in one memorable instance, electrocuting one, then lighting its tail on fire. Sissel even comments that he really owes that last one an apology. Considering he's a cat, that's saying something. The same sequence also has you dropping a chandelier on someone's head and hoisting her up to the ceiling with it.
The Nancy Drew game Legend of the Crystal Skull requires for Bess to snoop through the back room of Lamont's shop. Doing this requires doing things like giving Lamont diarrhea from spicy gumbo and sending him into a sneezing fit, as opposed to other games where all you had to do was just wait until the suspect was gone.
In Shadow at the Water's Edge, Nancy can't solve the mystery unless and until she upsets several suspects by bringing up a relative's death more than once.
One puzzle in Stupid Invaders involves finding a delirious Santa Claus trapped in the chimney, and getting past him by dissolving him into a puddle of goo with toilet bowl cleaner.
The Cave is all about your merry band of spelunkers doing dreadful things in order to progress through the cave and claim the thing they want the most, whether it's screwing a prospector out of his gold, pushing an explorer into a spike-lined pit, or launching a nuclear missile that will kill a hundred million people.
Blazing Dragons: At one point, you come to a psychiatric clinic that features, among other people, Rapunzel and the Pied Piper. Rapunzel is afraid of having any hair on her head and the Pied Piper thinks he must constantly play unless the rats come. What do you do? Use fast-grow hair tonic on Rapunzel and plant termites in the Pied Piper's pipe so they'll eat it.
In Runaway: A Road Adventure, you meet an artifact restorer who takes pride in her work and the fact that she hasn't destroyed a single artifact in her entire long career. You need her to restore something you have, but she won't do it until she finishes the work she has (which is a lot). You advance the plot by tampering with her equipment, causing her to break the item she's working on, which in turn causes her to have a mental breakdown.
Back to the Future has a few examples therein, but the shining example is serving a barrel of illegal hooch to a set of reformed alcoholics.
First Person Shooter
In Portal, you have to incinerate your best friend the Companion Cube at the end of the test chamber to continue the game; GLaDOS won't open the door until you do. However, the only noticeable difference between the Companion Cube and every other (completely inanimate) Weighted Cube in the game is that the Companion Cube has pink hearts painted on it, and that GLaDOS discusses it in a way specifically designed to make you feel guilty.
In Portal 2, GLaDOS plays with this trope again by 'fizzling' a large number of companion cubes in a certain chamber, proceeding to claim that she 'thinks that one said 'I love you'. They are sentient, of course. We just have a lot of them.' It's not entirely clear whether she's lying, as the Companion Cubes in this game do appear to... sing... when you're near them.
In the same game, when Wheatley detaches himself from the rail, he asks you to catch him — but you can't, no matter how hard you try. During his Villainous Breakdown at the end of the game, he brings this up as proof of what a horrible person you are.
At one point (near the end of the level "Sick Ward") you have to activate a switch which will open a necessary door... and simultaneously activate flamethrowers inside prison cells, burning several innocent civilians to death.
Call of Duty: Modern Warfare 2: the third mission in the game involves being an undercover special ops soldier in a group of Russian terrorists, and joining them on a massacre of hundreds of innocent unarmed civilians in a crowded airport. You don't have to participate, but the best you can do is to watch the other terrorists doing it without lifting a finger to prevent it. Oh, and then you're still forced to kill the SWAT teams that quickly show up to stop you. Interestingly, when you first start up the game, it offers you the option of skipping this mission entirely, knowing that it will probably shock and disturb a lot of players.
Early in Borderlands 2, Claptrap tries to open a gate, fails, and tells you to man a nearby gun to blow up the gate. All well and good. He then tells you not to fire the gun until he moves out of the way. Despite having several minutes worth of dialogue telling you to wait for him to move out of the line of fire, he never actually moves, and you have to blow up the gate while he's standing next to it. Played for Laughs, as Claptrap is The Chew Toy, and is none the worse for wear afterward.
Later on, there's the whole "clan wars" series of sidequests, which involves triggering a gang war between two clans and spending a few missions taking jobs from both of them. Said jobs involve doing things like trailing one clan leader's son and gunning him down, setting fire to people's trailers while they're still inside, and then crashing the funeral of the guy you killed and killing everyone. Sure, both clans are Asshole Victims and Borderlands being Borderlands, the entire thing is played as Comedic Sociopathy, but it's still a bit surreal to be rewarded for stuff like bringing a shotgun to a funeral.
And you have to vary what you use to clobber the zombie or it becomes desensitized and its mood eventually stops dropping. It's a damn relief to buy the upgrade that increases the magnitude of mood alterations, because it is damn tedious.
In The Company Of Myself, your main character uses a simple platform game as an allegory of his thought process to tell the story about how he's insane and killed his wife for really no reason. In order to represent this, the game makes you kill his wife to solve a puzzle.
In Gyossait, you're forced to kill a girl by dropping a huge piece of metal on her head. You also must flip a switch that kills everybody in the room.
Some of the treatments in Die Anstalt can feel horrible to perform on the cute little stuffed animals, but are sometimes required to help the patient.
Dub is the best example; at one point you have to perform ECT on him, and at another you end up making him cry hard enough to go through an entire box of tissue. But you have to do both of these things to help him in the end.
Hack and Slash
This is, in effect, the entirety of the God of War series. Highlights include:
The infamous sequence in the first game requiring you to sacrifice a live soldier to solve a puzzle, with him wailing and begging for his life the entire time. This is the harshest example, but the game is full of this sort of thing.
Quick-time events in the second game forcing the player to smash helpless old men's skulls in as blood sacrifices.
Murdering everyone in Elysium in the PSP title.
About half the third game, including:
Burning a helpless prisoner in Hades to death while he screams and cries for help purely because you want the bow he offered if you freed him anyways.
Throwing helpless and terrified civilians to their deaths regularly.
The various grotesquely violent executions of the Gods, including beating victims to death with your bare hands, smashing in another's face until the skin is literally stripped from the skull, and pulling a crippled, helpless God's head off bare-handed seemingly just because you can. Then using it as a lamp.
Ninja Gaiden 3 has three sequences where you must slowly walk towards a helpless and disarmed enemy, with no other choice than to coldly and mercilessly cut them down. Only the first one − a Mook who just watched you decimate dozens of his comrades and drops his gun, pleading for his life − is scared shitless, while the other two dare you to kill them while lecturing you, but all of them are entirely defenseless in said sequences.
Infocom's Trinity required you to capture a skink (a lizard), only to kill it later on because a spell required as an ingredient "fresh whole lizard, killed in the light of a crescent moon".
In The Chancellor, you have to poison a friendly lamb and feed its body to a rock monster in order to enter a cave.
Zero Sum Game, where you basically have to be a dick and murder people, including your trusting sidekick Maurice, in order to win.
Rendition, by nespresso, but intentionally — you're a torturer.
In Varicella, you've got to kill all your rivals to win the regency, including betraying your country's army to bomb the General (or, just doing it yourself), and sending a remote-controlled car to crash on top of the King's brother..
In Choice of Romance, you can only unlock the next chapter by getting involved with the very married king, right under his wife's nose. You either stay on as the other woman or man, or steal him (and the crown) for yourself by having the queen either killed or discredited. Choosing to just discredit her still ends up getting her killed.
World of Warcraft has one quest in the game that just stood out as a WTF moment: In the Borean Tundra, you have captured an enemy mage, and the quest giver instructs you to extract information from him yourself, as his code of ethics won't allow him to personally perform the act. This involves repeatedly using an Agony Beam while he cries out in pain. Even further, after completing the quest, you can ask for another of the Agony Beams just to use it on him, for no in-game gain.
Another questline has you find three Horde NPCs that had been captured and are being held in a human town. They are happy to see you... until you reveal that you'd been sent to kill them for having failed. They all die pitifully, one of them begging for his life. At this point, you've probably killed a dozen people to get to the individual cages they're in, and it would be trivial to unlock the cage and point to the exit, but you're not given an option.
The Death Knight starting quests. Among other things, it involves killing innocent villagers (most of whom who beg you to spare them), turning miners into zombies, torturing enemy soldiers, and executing an old friend of the player character. There's no option to skip any of this. Mitigated somewhat by them being part of the Scarlet Crusade — a faction also hostile to the Alliance and Horde — but even so....
Justified in this instance, as you are a minion of the evil Scourge during this part of the game and have no free will.
RuneScape has several cases of these in their quests. One notorious example has a quest where you do multiple cruel tactics to move up the hierarchy of the Vyre society, from taunting an imprisoned widow about their dead husband (one whom you killed in an earlier quest), destroying a slave's tithing glass and getting him executed to entertain a bored Vyrelord noble for his favor, and top it off, you must commit mass murder of human prisoners to entertain the guards. Even after the quest, since you have the option of doing more cruel acts to get access to the highest rank possible, which is required for the Completionist Cape.
A pair of puzzles in Banjo-Tooie require the senseless destruction of an anthropomorphic ice cube couple.
Moreover, across Banjo-Kazooie AND Banjo-Tooie, the main characters are constantly harassing a camel named Gobi for his precious hump water, forcing him to move from world to world and across games.
There is one instance in the old Sega Genesis game Dynamite Headdy. In one of the early levels, you come across a pipe in the ground that shoots out strange little round guys called Happy Campers. You have to knock them over into a bar fixed adjacent to you, brutally impaling them (and they turn blue and stop moving afterwards), so that you can hop on their corpses to get over a wall. Do it again to reach an extra life!
Many of the secret bonus points require beating up Al Bino, a mostly harmless custodian (though he can do damage to you in one instance).
When Yoshi is hatched for the first time (most likely Happy Horse Bridge or Pipes n' P-switches) in Something, he says not to drop him in a pit. Mario does this to access either exit in Happy Horse Bridge.
In Tomb Raider Chronicles, one level has you infiltrate a high rise and there's a door that can only be opened with two key cards at the same time. Normally, you have to coax a worker to use his card in conjunction with yours to proceed. However, if you want to get 100% Completion, you have to kill the poor sod to unlock an alternate path, which contains one of the level's secrets.
The Soviet Campaign of Red Alert 1 started off with a massacre on a village that harbors escapees from a Sarin gas test. The ending FMV comes complete with an Empathy Doll Shot.
The Nod Campaign in Tiberian Dawn had numerous missions that had very little GDI and focused on destroying villages. Oum Hadjer being the most memorable.
The GLA Campaign missions two and three had you loot villages for the supplies the UN gave them and looting the whole city of Astana, respectively.
In Rome: Total War, this is often the best way to deal with an overpopulated city. Overpopulation leads to rioting and increased likelihood of acquiring the plague. There is no standard way to "depopulate" a city... that is, other than pulling your forces out, allowing the city to rebel, and then recapturing the city. Once you've retaken it, you can "exterminate the populace."
Codename Panzers forces the player into this trope when the mission objective is "Kill All Enemy Units", as that last enemy Rifle squad gets cornered by the edge of the map and can neither run away any further, shoot back (as you're probably flushing them out with a tank or armored car), or surrender.
Role Playing Game
In Etrian Odyssey, Chieftain Visil orders you to kill the forest folk. Not much you can do about it, especially since you have to kill about twenty of them to get at the fourth stratum's boss.
This is both pointed out and made less reprehensible in the remake's Story Mode. It turns out that the corruption of Yggdrasil's core is causing a contagious disease that causes the Forest Folk to mindlessly attack anyone in their way, and it's incurable. Killing the infected is the safest thing for everyone. Nobody in the party is particularly happy about this, but it's a lot better than the implication in the original that all the Forest Folk you killed were just trying to defend their homes.
Agarest Senki has a sudden Difficulty Spike part-way through the third generation with the introduction of the boss Midas. He, and nearly every boss after, will have large area-of-effect attacks that will wipe out your party and a Healing Factor that negates most damage. Now, when a character dies, everyone else gets a huge amount of SP, which is used to fuel EX-skills...which are your only hope of killing those bosses. So what do most players resort to? Throwing their tank at the boss to keep them away from everyone else, letting the tank die, reviving them with their healer, and repeating until enough SP is stored to unleash hell.
Fallout 3 has many examples in the (story questline) 'Tranquility Lane', where the more obvious means of progressing the story is to visit torment on each of its residents, sometimes offering a variety of creative methods to achieve this. The good, more difficult way to finish this quest is to activate a failsafe that kills them all. It's a Mercy Kill, given the situation, but as far as they know, they're being gunned down in their homes by Chinese soldiers. The "good" option also forces you to leave the sick mastermind behind the whole thing alone in his simulation for eternity.
Fallout: New Vegas has a couple of examples that stand out in the main story quests as well:
Mr. House's story route requires you to wipe out the Brotherhood of Steel's underground bunker. And I mean, either, personally kill each and every last person there, or activate the bunker's Self-Destruct Mechanism. He absolutely, positively will not even entertain the idea of any other kind of solution (though he does have his reasons, granted).
It was originally possible to pass a Speech check to convince Mr. House to leave the Brotherhood alone, but it was Dummied Out. However, a mod exists that restores this option.
The other three ending paths will, at one point or another, require you to infiltrate the Lucky 38 and either execute a defenseless Mr. House in cold blood, or, if you're feeling particularly bastardly, leave him alive, but disconnected from his computer network and slowly wasting away from infections that he is no longer able to fight off.
In The Elder Scrolls III: Morrowind, the main plot requires you to buy a slave to serve as a wife to a tribal leader. She makes it clear she doesn't mind, but even after numerous plot-related killings, buying a slave can make some players twitch.
Given that her future husband thinks she's a high-ranking noble and will thus treat her as such, you're actually doing her a great favor, compared to the life she'd have had if someone else had bought her.
There's a city in Two Worlds that's supposedly surrounded by orcs, though they never appear outside the gates, and you have no opportunity to kill them. The only thing that's stopping them from getting in and killing everyone is a magical artifact under the city. In order to beat the game, you need to go underground and steal the artifact, and when you reach the surface, you'll discover that everyone in the city has been slaughtered by orcs. The best the player can do is complete a couple of quests that result in the quest-givers leaving town.
In Fable, there are two types of optional quests, good and bad. The bad quests can go as extreme as murdering every innocent civilian in an entire settlement in cold blood (who will beg for mercy and everything). The thing is, the game does not make entirely clear in the quest choice list which quests are "good" and which are "bad". You can accidentally choose a bad quest without meaning to. Ok, no such a big deal, just cancel it or don't complete it? Nope. Once a quest has been selected, there's no way to cancel it. If the location of the quest happens to be in your main storyline path, and there's no way around it, you are forced to do the quest, or you cannot proceed. Unless you have a savegame from before selecting the quest, you have no other option than murder all those innocent civilians if you want to continue the game, who will scream and beg for their lives and ask you why you are doing this to them. Good luck having a good night's sleep afterwards.
In Skyrim, the more vicious Daedric Princes order you to do horrible things for their artifacts (and you need to get all of them for an achievement). They usually involve betraying a companion or leading a good person to a horrible death. The less said about the things Namira, Molag Bal, Boethiah, and Vaermina demand of you, the better. That said, all of those are sidequests, and therefore don't have to be completed by the player unless you really want the rewards... although, the in-game rewards for these quests are good. Reallydamngood. Namira and Vaermina's quests, at least, can be intentionally "failed" if you're not quite ready to step over the Moral Event Horizon. In Vaermina's quest in particular, many players have flat out found themselves unable to complete it and therefore miss out on the "Oblivion Walker" achievement because it involves betraying the very likable Erandur.
However, they're not the only morally dubious things required for 100% Completion:
Thieves Guild: There are three achievements tied to completing the guild questline. By the time the guild questline has finished, the player will have robbed at least dozens of innocent people of items and money worth thousands and thousands of gold. It's not killing people, but it's still loathsome. Furthermore, the way the game works encourages the player to rob people blind, as theft is by far the simplest and easiest way to get material goods you want or need.
The Civil War Questline, another three trophies. This one can be YMMV, as plenty of people have no qualms about supporting one side or the other after looking at the situation fully — but other people see a situation with no good choices, only "less horrible" ones. Much like real wars in that respect, yes, but still depressing.
The Dark Brotherhood questline has another three achievements. And the Dark Brotherhood is, not to put too fine of a point on it, a quasi-cult that listens to a mummified corpse of the bride of the void god Sithis, who tells them which people to kill. The player's kills, if they follow this questline, include a man driven to insanity from his sister's death and a bride on her wedding day, among others. The player character is encouraged further to do these despicable things by great in-game rewards, such as access to Shadowmere.
This one at least has a slightly non-evil ending available; if you kill the member of the Brotherhood who kidnapped you at first (yes, still killing, but she's an unrepentant assassin trying to force the player to kill one of three people, two of which are totally innocent, and she doesn't care about the choice so much as the murder), you instead get a quest to wipe out the Dark Brotherhood — still violent, but probably for the good of the world.
There's an achievement for having a bounty of at least 1000 gold in all nine holds simultaneously, for which the player must get caught doing horrible things — for example, killing people. And then there's an achievement for escaping from jail, which of course requires going there in the first place. These, at least, can be acquired by — just as an option — assaulting chickens rather than actually hurting people. Or for the jail one, you can simply try to pick a lock when a guard's nearby, for a 5-gold bounty.
In short, the game is so structured that while excessive cruelty is not really required to beat the main quest, the main quest is itself a very small part of the game as a whole, and the player is practically stuck with only half a game if they choose to play a Dragonborn who's actually a decent person.
Solatorobo: At one point, your character enters Super Mode and takes out the two enemies that had been plaguing you. They've recognized their defeat by that point, and there is no point in attacking further... But you have to destroy their mech (and them) to continue.
Stealth Based Game
In Dishonored, the only way to complete a Pacifist Run is to impose a Fate Worse than Death to all the important characters except Daud, as sparing him is clearly shown as an act of mercy. Two of them clearly deserved it, the Pendleton Twins probably deserved their fates as well, but Lady Boyle is shown as quite a nice person, has nothing to do (for what we know) with the Big Bad's crimes, and her only "crime" is to be rich (something you can't really reproach her, as the Empress' former bodyguard). You still have to either kill her or give her to a Stalker with a Crush, who's implied to keep her imprisoned for the rest of her life. For some reason, you can't just abduct her, or draw your gun and scare her into betraying the Big Bad.
The ending of Metal Gear Solid 3: Snake Eater. After you hear the Boss' detailed and incredibly noble reason for the Fake Defector "betrayal", you're asked to do the only thing available to stop the whole sordid affair from being entirely pointless. So you, the player, get to shoot the world's greatest hero in the head.
The Neighbours From Hell series is based on this trope. The player is a Reality Show participant whose task is to cause a neighbor the maximum amount of grief in order to get the highest ratings. The second game adds the neighbor's mother and her dog to the list of acceptable targets. Granted, the neighbor is a jerk, but this seems a little excessive.
Horror game Penumbra: Overture is fairly standard storywise until the very end. Red, a mentally unstable man who communicates with you via a one-way radio, continually talks to you about the moment you two finally meet. When you do finally get to him, he's locked himself in an incinerator, and begs you to turn it on. He's swallowed the key you need to proceed. It's arguably a mercy killing, but it is necessary, and his screams will give you nightmares for weeks if you took a shining to his quirky personality.
The entire premise of Manhunt is to sneak up behind people and kill them in the most gruesome manner possible with objects you find along the way.
Granted, most of the enemies in The Last of Us deserve what's coming to them, but Joel is eerily nonchalant about it most of the time. The rest of the time, he's either irritated or pissed. You're not exactly playing as a saint...
To clarify, you end up killing resistance fighters looking for a way to save humanity and well-mannered, civilized people despite their hebephilic leader and...um...diet. Whether or not it's worth it...
We're shitty people, Joel.
The RPG Maker game The Witch's House has a lot of these. Most notably, you pick up an affectionate frog who helps you with several puzzles which you must then feed to a giant snake. Part of the reason for this is to draw the player into the horror of what is going on in the house. Another is to foreshadow that you're playing as the witch herself, and that's why she's so cruel.
Third Person Shooter
A "good" variation of this occurs in Shadow the Hedgehog, which has several areas where you're required to attack a flying Black Arms creature to be able to ride on it. This earns you points on the good side of the Karma Meter, but you have to do it even if you're trying to accomplish the evil mission. The Big Bad will even yell at you for doing so even though it's required to progress.
This happens a strangely large amount of times. In the first level, Sonic says he doesn't wanna anger GUM, but homing attacking the flying bots is the only way across. Naturally, he yells at you for doing this. It gets even worse when Amy/Espio is yelling at you for destroying Eggman's robots. Even when Eggman is currently in the process of trying to kill you.
Spec Ops: The Line — Using the whitephosphorus on the civilian refugee camp is the only way to advance the plot. According to the developer, the only alternate option is quite simple — stop playing the game.
Turn Based Strategy
Fire Emblem: Shadow Dragon, in a mild variation, forces the player to sacrifice one of their early-game characters in its Normal Mode tutorial chapters. There are other ways around that, but they involve even more characters dying in a game where death is permanent and useful characters are a very valuable resource. Most players just throw Crutch Character Jagen to the wolves.
That being said, the remake-sequel for this game, New Mystery Of The Emblem, reveals that the character who was the canonical sacrifice, Frey, actually survived the ordeal but lost his memory for some time (explaining his absence up until that point). Of course, if you prefer to play Hard Mode, you won't play through the prologue chapters anyway.
In CyberStorm, Bioderms are to be viewed this way and some of the HERCs' weapons systems compels you to use the Bioderms as suicidal missiles to take down nastier Cybrids and HERCs, as they all have a limited lifespan and you can simply breed more of them.
In the RPG Maker game OFF, by Mortis Ghost, the player is more or less tricked (or forced to progress the story) to kill each one of the leaders of the zones he enters, including The Batter killing his "wife", the Queen, and Hugo, a helpless infant and the one who created both he and The Queen in the hopes of creating a bright future.
Wide Open Sandbox
It's theoretically possible to avoid killing innocents in Prototype, but in practice, your civilian kill count will likely number in the hundreds within the first hour of gameplay even if you don't deliberately attack them, simply because they're everywhere and oh, so fragile. Trying to get through a fight without any collateral damage will almost always result in failure, especially if you're driving a tank around. And the easiest way to regain health is to grab the closest person and smash them open before absorbing their biomass. You don't have to... but gosh, wouldn't that extra health be useful...?
Also, if you accidentally grab an innocent civilian, it is impossible to let go of them without hurling them a few blocks.
The now-infamous mission "By the Book" from Grand Theft Auto V, in which the player is forced to torture (quite graphically) an informant who has information about a target the FIB wants to assassinate. What firmly drives it into this trope is the moment after the fact, when Trevor off-handedly remarks that he knew the torture was ineffective and that he was pretty much doing it for fun; this is likely the exact opposite thought of what's running through the player's mind at that point in time.
In order to continue with the game in Terraria, you need to throw a doll into the lava of the underworld. A VOODOO Doll of the Guide, killing him in the process so you can summon the boss to advance. Skeletron can be re-summoned by equipping a Voodoo Doll of the Clothier and finding a way to kill him.
Most items have "tooltips" that tell you a little about them. The tooltip for both of the voodoo dolls is just "You are a horrible person."
About half of the Brotherhood quest chain of Saints Row 2 is an escalating prank war that turns deadly about halfway through. An early mission involves stealing toxic waste for use as tattoo ink. Later, you kidnap the Brotherhood boss's girlfriend, lock her in her own car's trunk, and abandon her car at a monster truck rally for her boyfriend to run over. Yes, these people are violent jerks, but it's still unnecessarily cruel.
On the other hand, the aforementioned trunk locking is done as retaliation after the Brotherhood kidnapped one of your lieutenants, chained him to a truck bumper, and took him for a drag through the Stillwater docks. After which he is so badly messed up, your character is forced to give him a Mercy Kill. The toxic tattoo is a dick move in response to a ridiculously low-ball offer made by the Brotherhood's leader to split Stillwater between his gang and the recently reborn Saints.
In Saints Row: The Third, the Boss can do this unintentionally. If someone is too close when you press the action button intending to open a door, participate in a photo op, or get into a car, you grab them as a Human Shield. Unless you're near a body of water or a short ledge, your only options at that point are to either kill them with a Neck Snap (or throat bite if you have a certain DLC), or throw them. They might live if you throw them, unless you've gotten the melee-muscles perk which can make them fly over a hundred feet.
The "Ho Boat" mission involves stealing a shipment of prostitutes from the Syndicate, at which point you can either sell them back or keep them to add to Zimos' stable. The option of simply letting the innocent, terrified sex workers go free is not available at all. However, the consolation you get for keeping them is that it is established that Zimos treats his women very well and even lets them unionize.
In Bully, a lot of the unskippable missions involve you acting like a complete Jerkass (hey, it's in the title). In one, you have to sneak several racy pictures of a seventeen-year-old girl and post them up all over town. In another, you have to plant evidence to get a teacher fired. In yet another, you help the gross cafeteria lady Date Rape the chemistry teacher.
Other / Unsorted
The Path requires you to make your character waltz right into the Wolf. And if you played the game right, you have to do it only after really starting to care for the character as soon as you learn everything about them.
In Tiny Toons: Defenders of the Universe, you have to beat up FifiLaFume at one point to continue. The reason? She is trying to stop you from doing something that she and Shirley have foreseen will lead to the Earth being doomed. Even though Babs (her best friend) and Hamton (her boyfriend) are present, they don't even try to talk her out of it. Turns out she was right.
In Katamari Forever, the King of All Cosmos spends most of the game out cold, while the Prince and his cousins build a RoboKing to help rebuild the Cosmos. Once the King reawakens, he immediately orders you to dismantle the RoboKing, rolling him up piece by piece. (But don't worry; the Negative Continuity of the game ensures that he'll stick around.)
A quest in The Sims Medieval forces the monarch to kill his/her advisor, even though the player is given reason to believe the advisor did nothing wrong. Thankfully, he gets better. That is, he'll come back in your very next quest. So will your ship, which you blow up with the advisor and servant on it. But still.
In Pharaoh, the best way to keep your city happy and well-fed is to have is to stick a few houses near the various industries (which no one wants to live next to) without setting up the usual services (health, food, clean water...) as trying to keep everyone on a more or less equal footing is expensive and counterproductive (the available labor force is taken from housing as a whole, so as long as there's one house in range of a recruiter, the industries will work regardless of its level). This mechanic was done away with in subsequent games, probably as a direct result of the above.
In EmperorRiseOfTheMiddleKingdom, if you're trying to get things done in time and you only need a population level, it can be easiest to simply build up a developed central town and then just create endless shantytowns outside the city walls. At least that's historically accurate, though.
In NCAA Football, the game makers mistakenly included a hard roster limit, preventing you from stashing players to develop. However, you are also in competition with the other teams for recruits, so if you deliberately limit yourself to open roster slots, the opposing teams will get stronger. So a common, almost necessary strategy is to heavily recruit some poor 17 year old all through his senior year of high school until he chooses you over your rivals. Then cut the poor boy before he even puts your jersey on once. Those recruits disappear from the game entirely.
You don't need to look further than the title for KZ Manager.