Even better, if you piss off the pig at Link's home island after it grows to full size, it does more damage per hit than anything else in the game.
In the battle mode of The Legend of Zelda: Four Swords Adventures, this is actually a sneaky tactic — Attack a Cucco inside a building enough times and a swarm of them will appear and attack your pals; since they do not attack anyone inside buildings, you're safe!
There's an interesting variation on this in Twilight Princess, where you temporarily control the Cucco you've been attacking.
In The Legend of Zelda I, hitting the old man with the sword or other weapon will cause the fires to shoot at you if you are in an underground dungeon.
In Oracle of Seasons, after defeating the King Moblin, you find him in a house in Sunken City, crafting bombs. You can throw a lit bomb or ember seed into his stockpile, then flee the house and watch it blow up with him inside of it. Try this repeatedly, and the third time he catches you and traps you inside the house when it blows.
Hilariously in Ocarina of Time, the chickens in Lon Lon Ranch can be run over while riding Epona. As long as you're riding her, the Cuckoos, or anything else for that matter, can't hurt you.
In The Legend of Zelda: A Link Between Worlds, not only are there both Hyrulean and Lorulean Cuccos that act this way, but you also get another case with a certain Hinox in a cave. When you enter, this particular one begs for mercy and offers Link money to leave him alone. Refuse the money, and he offers even more rupees, up until the end. Do it too much though, and he absolutely flips out and attacks Link, turning invincible and doing an absolutely massive amount of damage unmatched by pretty much any other enemy in the game (including the final boss). Bully and extort NPCs at your own peril...
In the NES game Nightshade, you are a superhero. You gain reputation for defeating mooks, and the more reputation you have, the more people will help you. Very high reputation yields such rewards as a healing booth (which you will need). Attacking someone defenseless, however, causes your reputation to take a nose dive.
Beyond Good & Evil lets you fire on friendly boats and airships from your hovercraft. However, if you keep shooting at them, they'll eventually call the police on you, who will fine you. Some NPC ships are quicker to phone the cops than others... And if you maneuver quickly, you can actually avoid the police!
In Star Fox Adventures, repeatedly attacking Tricky with Krystal's staff early on has no repercussions. However, doing it too many times after he's learned the Flame command results in him attempting to set Fox on fire.
Although you can use that to your advantage to save on GrubTub use. (Not that you really need to; you can stop collecting them ever again stupidly early without that trick and still have enough to finish.)
In the Superman Returns game, you don't have a life meter. Instead, the town does. So even though you can interact with just about everything, doing so with the intent to destroy can "reward" you with a Game Over.
There was a Mission: Impossible game for the NES that fit this trope. If you killed a civilian, a helicopter flies in from nowhere and captures your current character, which has the same effect as killing him.
The Goonies II allowed you to strike friendly characters with your fists or a hammer. If you hit certain characters, though, they refused to help you in the future.
In the first Soul Reaver game (which is the second Legacy of Kain game), civilians and vampire hunters will fall on their knees and worship you — even let you feed on them — unless you start killing them, in which case the civilians will run away and the vampire hunters will attack you. They're not especially dangerous, but they can be inconvenient.
Although not as severe as some of the other punishments, biting some of the larger animals (specifically the tigers and bears) in Ōkami will cause them to attack you.
In The Legend of the Mystical Ninja, attacking innocent people in towns will cause a swarm of angry guards to assault you. They will keep spawning unless you leave the area.
In Tomb Raider II, attacking the Tibetan warrior monks in the Barkhang Monastery will result in every single monk in the entire level going for Lara's blood — and it can be easily done if the player is simply trying to help the monks out in their fights against Bartoli'smooks and accidentally target a monk instead of a gunman. They aren't hard to kill, but since there's so many of them it can be easy to become overpowered. Also, they can be a huge help when they're attacking enemy mooks instead of you.
There is a similar situation in Tomb Raider III at the High Security Compound, if you do the All Weapons cheat to circumvent your lack of weaponry and shoot at the prisoners who are fighting the guards. There is at least one prisoner who is completely invincible even to rocket launcher blasts.
Sort of a minor one in the Nintendo DS version of LEGO Batman: Once you unlock Alfred as a character, he'll usually be peaceably standing around as an NPC in the batcave. You can attack him, but once you do, he'll come after you with a bat.
Oddly enough for the theme of the game, Overlord 2 punishes a few specific instances of vandalism, which it usually rewards. In the Empire Slums/Sewers area, some destroyable houses block off drainpipes that, when unblocked, endlessly spawn giant frogs, which can devour your minions, killing them regardless of health, level, and equipment without chance of in-combat resurrection. So, in this one area, you're better off destroying as little as you can.
The Warriors punishes players that attack their own allies by having them turn against the player for a while. They attack much harder than any Mook and Elite Mook in the whole game. What makes this funny is if they kill you and you have some flash on you, they will revive you, even though they just finished kicking your ass!
In Nancy Drew: Danger on Deception Island, it's possible to give Nancy and Katie food poisoning. You can make Nancy a sandwich that turns out to be the most volatile sandwich ever created (such as putting jellyfish, ice cream, mayonnaise, tomatoes, and peanut butter on a sandwich) or have her give it to Katie. However, this gives you a game over. It's actually the mayonnaise that's the bad thing, since it expired in 1994 (for context, the game is presumably set in 2003). BLEGH.
For that matter, doing cruel things in the games (especially to Nancy) almost always gives you a game over. This is inverted in Danger by Design, where you can get someone fired but are merely given a Bittersweet Ending, and in Legend of the Crystal Skull, where you are required to do some rather mean things to a poor shopkeeper in order to complete the game.
Most recently, in Ghost of Thornton Hall, Nancy can leave up to three people to die in a fire, but the endgames that result are less fulfilling and explanatory than the Golden Ending.
Although you can get past this. Kill someone you don't need to anymore and watch as they make a very overly-dramatic death animation. Drop all your items down, and the guardian will take away your nothing. Then you can pick up your items, drop them, then go on a killing spree.
Attempt too viciously to get into Katrina Gibson's pants in Snatcher and she will throw you out.
In Little Big Adventure 2, you are able to go into the kindergarten and attack small children. However, the moment you leave, their older brothers will be waiting outside to take turns in beating you up.
Below the Root takes place on a planet where the society is very strictly pacifist, and so orderly that Kleptomaniac Hero is utterly averted as no one thinks of just walking in and swiping another person's stuff without permission. At some point, you can potentially get a sword-like object, the wand-of-Befal, from a rebel group called the Nekom. If you use it for any purpose other than hacking down plants (i.e., killing people or animals), you lose spirit points permanently. Spirit points give you various magical powers as you get more of them, and it's possible to make the game unwinnable if you lose enough of them.
It's worse than that. Slaying a human will strip ALL of them away from you, as a warning that you just crossed the Moral Event Horizon. This is guaranteed to make the game Unwinnable if you've managed to progress that far.
In the Homestar Runner game Peasant's Quest, attempting to attack the horse will result in you getting killed. You still have to spook him to progress, though.
Lowering the baby down the well and then leaving the screen would kill you. The game doesn't even bother with an explanation, it's just so disgusted with you that it won't let you play any more. Throwing the baby in the lake does not have this consequence, but only because he's an amazingly skilled swimmer for his age.
In Déjŕ Vu, shooting any person besides one specific NPC results in either the cops hauling you off or your intended victim being faster on the draw.
In the first game, you can kill people with the syringe, and get away with it; until the police catch up with you. Since you have to speak to the police to win the game, killing any innocent makes the game unwinnable.
Stealing Weird Ed's hamster in Maniac Mansion is required to complete the game. Giving it back is optional. Also optional is exploding it in the microwave. If you give it back to him at that point, he will kill you. This is highly likely to render the game unwinnable; if you had required items in that kid's inventory, you won't get them back.
In Heroine's Quest: The Herald of Ragnarok, you can follow the standard adventure game logic of taking anything that's not nailed down. If you take the wrong item, however, you will find that none of the human characters, who before may have been praising you for your heroics, now consider you a despicable person and refuse to talk to you, demanding that you leave. If you make the (not very difficult) leap of logic that the item you picked up is causing this, you might think to restore a save game from before you grabbed it. Then the game specifically states that the item jumped across save games to follow you.
Shooting the scientists, but not killing them completely, may cause them to shoot you with the DD44, a powerful handgun.
The easier difficulty settings in GoldenEye allow you to 'accidentally' (heh heh heh) kill some civilians and scientists and not fail. Thus, wound a scientist, wait for him to pull his powerful gun, and then kill him. Sometimes this allows you to swipe grenades.
More amusingly, in Soldier of Fortune 2, doing likewise will cause John Mullins to spontaneously die.
It may have been a bug, but killing too many women in Soldier of Fortune would cause all their death sounds to start looping incessantly, sounding like hell itself.
Likewise, killing a civilian in Halo: Reach causes Noble Six to spontaneously drop dead.
Deus Ex has a minor one: if you took the violent approach and shot up NSF rebels, your armorer will reprimand you and remind JC that the UN troopers are peacekeepers first and soldiers second, and will withhold extra lethal ammo, instead giving you the multi-purpose multi-tools.
In Marathon 2: Durandal and Infinity, blasting enough humans or S'pht'Kr results in them turning against you. This was carried over to Marathon's Spiritual SuccessorHalo. Worse, in that game, killing any innocents in the first level results in invincible marines attacking you.
Security guards in Half-Life will attack you if you start killing them. In both expansion packs, killing friendlies before the game proper starts (during the training course in Opposing Force or during the prologue in Blue Shift) results in immediate Non-Standard Game Over.
SUBJECT: Adrian Shephard
STATUS: Awaiting court-martial
A similar technique is used in the original game if you kill some NPCs vital for game progress:
STATUS: Evaluation terminated
POSTMORTEM: Subject failed to effectively utilize human assets in achievement of goal
Metroid Prime 3 has soldiers and maintenance workers in the first area that you cannot harm, but if you keep shooting them, a turret appears and the ship's AI warns you to cease fire. Shooting more or shooting the turret will cause it to fire at you. Wreck it, and a stronger one appears. Wreck that one and an even stronger one appears that will instantly kill you, can't be destroyed, and you can't dodge its attack.
Also, don't shoot Bruno's corpse. Although if you do, you'll probably figure out a twist coming later...
Call of Juarez prevents you from corpse-beating (shooting or hitting dead enemies), and even causes an immediate game over if you somehow manage to do it. This is actually plot-relevant, as at the very end of the game, the Big Bad only appears to be dead after the first time you fight him; he returns for more shortly afterwards. The Video Game Cruelty Punishment prevents you from shooting him in the head while he's down and making him dead for real.
While Duke Nukem can kill lap-dancers in Duke Nukem 3D, his reward is only to get more enemies to spawn.
Operation Flashpoint is a bit more lenient than most: you can "accidentally" kill one or two of your teammates during a firefight before the rest gun you down, but if there are no enemies nearby when you kill a teammate, you're as good as dead.
In SWAT 3, your fellow officers will immediately shoot you if you kill any of them.
In SWAT 4, you can fail the mission by shooting the bad guys too much or without warning.
In Halo: Combat Evolved, if you kill your captain in the first mission, you'll be locked inside the bridge and a squad of invincible marines will rush in to butcher you.
In the hands of a pair of bored teenagers who played HALO too much, this becomes the ultimate boss fight.
Throughout all of the Halo games, killing enough marines will get them to turn against you and kill you. The exception is the plot-important ones with Gameplay Ally Immortality, as you can't kill them — but they will still turn against you if you kill enough marines, and it's still impossible to kill them.
In Call of Duty World At War's DS version, meleeing an ally will result in him returning the favor — killing you in one hit.
Inverted in Modern Warfare 2. Trying to save the civilians in the infamous No Russian scenario by killing their attackers nets you an instant game over. Likewise, trying to block their line of fire by standing in front of them will result in them just shooting you. The most you can do is not actively participate in the slaughter.
In the German/Japanese version, this is all you can do. Shooting the civilians nets you an instant game over, as well.
And in the first Modern Warfare game, there's a point in one mission (the one that flashbacks to 15 years ago) where you encounter a wild dog, which your partner tells you to simply avoid. If you decide to take "Shoot the Dog" too literally here, well... the end result is the dog's pack swarming you, like the Cucco Revenge Squad only with ANGRY DOGS. While a little luck and a little skill will see you and the Captain through, it's just a pointless waste of time and risk. Your partner berates you as such if you survive.
Killing a critical NPC obviously fails the mission ("Friendly fire will not be tolerated!"), but you don't get punished for accidentally hitting Red Shirts.
Oddly enough, you can get away with murdering the crew by proxy through using the console to spawn enemies. Make sure you use the invisibility cheat so as you're not targeted (by either side, as sometimes the crew will go crazy and start shooting you when this happens, and security can also beam in), and let them wipe everyone out. You can then proceed to finish off the enemies yourself. For the rest of that Virtual Voyager game, anyone who died will remain dead on the floor, even if you leave the area and come back. Note that doing this can prevent you from getting 100% completion, so only attempt this after you have.
Shogo: Mobile Armor Division has one. If you shoot at your commander in the opening level, he'll give the order "Kill Him," and a group of soldiers will rush you and continue to attack until you're dead.
Clive Barker's Undying: Yes, the remaining servants are doomed. No, that doesn't mean it's okay for you to shoot them.
Somewhat utilized as a game mechanic in BioShock. Killing a Big Daddy in order to get to the Little Sister they're tasked with guarding results in the lovely image of a six year-old girl sobbing over her father figure's corpse. Kind of hard not to feel like a jackass, there. In BioShock 2, harvesting a Little Sister after you adopted her will net you a heart-wrenching "DADDY! NOOOOOOOOO!!!!" Also, Little Sisters you meet afterwards will act afraid of you and ask if you're going to hurt them.
In addition, killing the Little Sisters in the first game actually makes the game more difficult than sparing them. Killing the Little Sisters gets you the most ADAM at once. But sparing them ultimately nets you more ADAM from Tenenbaum's gifts that she'll send for sparing every few Sisters. On top of that, some powerful plasmids can only be obtained in these gifts. So, the only reason to kill the Sisters is if you feel like being a jerk.
Lampshaded in Serious Sam 2 in the Kleer planet. After dispatching some Kleers who are burning a giant doll of Sam on a stake, shooting the doll itself damages you and causes Sam to exclaim "I knew it. I KNEW IT!"
Also in The Second Encounter, where one secret takes you to a miniature set of the final level of the first game. Blowing up all the scenery and props nets you some items, but if you so much as touch where the mini-you is? Instant death.
Portal 2 also inverts this with GLaDOS specifically telling you that, since the puzzle room exit does not contain an emancipation field, you should not abuse the opportunity to grant the companion cube freedom. Despite having the player expressing care more than cruelty, she still punishes you by detonating it in your arms.
GLaDOS: I think that one was about to say "I love you".
Redneck Rampage has you end each level by hitting your brother with a crowbar. Shooting him instead has the game kill you a few seconds later.
Killing any innocent programs in TRON 2.0 will end your game immediately with the now-legendary "This program has performed an illegal operation" message.
Left 4 Dead does not have any system in place for people who intentionally harm and team kill other players, but some 3rd party servers have modded systems in place where any intentional friendly fire is reversed back to the shooter, making the player hurt himself instead of his target, and other servers will instantly kick or ban players who try to grief others this way. Depending on the griefer, they will try to get themselves killed anyway to hurt the team.
For people who are not griefing others but are tired dealing with the less than stellar survivor bots, killing a survivor off makes the game a lot harder since now you are down one player and are more vulnerable to attacks from zombies.
The Chronicles of Riddick: Escape from Butcher Bayallowed you to kill many of the inmates you encounter, primarily in Single Max. It becomes much more difficult in Double Max; attacking any of them that are in the vicinity of gun turrets just means the player is Too Dumb to Live, but it can still be done. Triple Max really exemplifies this particular trope, however: you are dropped into a small secluded room for daily exercise with an incoherent and unresponsive inmate, whom you can easily kill. Doing so results in the Butcher Bay computer announcing that you have been sentenced to death, and it starts injecting kill poison into your bloodstream through your cryogenic suit.
PAYDAY: The Heist has a punishment system in place for players who go out of their way to kill civilians (or done by accident thanks to the lemming behavior of the civilians). Every civilian killed adds a 5 second delay to your negotiations for your release should you be apprehended by the cops and each civilian killed incurs a monetary penalty at the end of a successful heist, which can make leveling up more tedious.
Far Cry 3; if you choose to make an evil choice in the end, karma ends up punishing you for it. Whereas if you make a good choice, karma ends up punishing the source of punishment in the former.
Also, attacking any friendlies, or even just driving into their car by accident, will result in all allies in the area turning on you. Thankfully, this doesn't follow over after you've killed/evaded them.
In Shadow Warrior (2013), there ARE no friendlies outside of cutscenes, only demons and yakuza, but there are the neutral critter bunnies. Killing them is totally ok, except when they're having sex. Then you only kill one of them, and the other turns black and glowing, gets insanely fast, metal music starts playing and it starts beating on you. It's got a moderate amount of hit points, does minor damage which is healed fairly easily, but the damn things are so fast that you can barely hit them.
More than that, using Planet Busters (or just excessively damaging the environment in general) is a bad idea — when you hit the planet, the Planethits back, sending a nearly overwhelming swarm of its worst mind worms to chew through your bases' defenses. In Alpha Centauri, the planet destroys you.
"Minor" atrocities like using nerve gas, using biological warfare, or nerve-stapling or destroying base populations, will result in the planetary council imposing trade sanctions against you, and the faction you committed the crime against will almost certainly remain your sworn enemy for the rest of the game.
But note that you can avoid most of this by repealing the UN Charter. This makes "Minor" atrocities legal, although Planet Busters still cause all-out war and planet despoilment still causes Planet to go berserk on you.
Using nuclear weapons in Rise of Nations reduces the "Armageddon Clock". Too many means the game ends in apocalypse.
That seems similar to the nonstandard game over of the game Balance of Power (a RISK-esque political game where you play the US or the USSR for political influence). Whatever one player does, the other player can challenge in the UN, and escalate tension. The idea is that one of you two will eventually back out (and lose prestige). However, this can lead to a nonstandard gameover with the message "You have triggered a nuclear war, and no, there is no animated gif of a mushroom cloud. We do not reward failure". This also happens if tensions are too high and an accidental nuclear war triggers.
Games produced by Paradox Interactive actively encourage you to be ruthless and kill people.
In the Europa Universalis III, there is the 'raze' option, by which you could order your armies to raze a territory. Doing so drastically lowers taxation and production income in the province for years, as well lowering the territory's manpower contribution for years to come.
World of Warcraft (and probably quite a few other games) used to have a thing called Dishonorable Kills. If you killed a player of much lower level than you or an NPC marked as a civilian, you would be given a dishonorable kill, which would affect your rank. This got removed a couple years ago, though.
In fairness, it should be pointed out that Blizzard encourages a certain amount of this by including achievements for killing certain NPC members of enemy factions; a lot of the time, other NPCs get caught in the cross-fire.
In the Wrath of the Lich King expansion, there's an achievement you can get by killing fifteen turkeys in three minutes, and there are only a few places where there are enough of them to make it possible. Completing this achievement causes all turkeys and many other formerly nonaggressive creatures to become hostile to you and flocks of enraged turkeys will occasionally spawn and attempt to peck you to death. Fortunately (or not), the effect is temporary, and it's nearly impossible for them to kill a character who's of a sufficient level to belong in the zone.
There is some punishment that this player found out after getting the achievement. The first day of release, player goes to get the turkey achievement. Afterward, sees that all enemies are hostile and is delighted since being a hunter with a gorilla that means easy grinding XP on the normally neutral mob packs. Get to an area with a quest NPC that is a dryad and does not offer quests as they are neutral. As well all the other normally friendly/green dryads become attackable NPCs. Was really annoying first time through and took the player a little while to figure out what happened.
Killing normal animals (in self-defense or otherwise) in the Borean Tundra of Northrend will cover you in their blood, and the usually friendly Cenarion Expedition druids in the area will attack you until it dries after 3 minutes or you wash it off in a body of water. They have no problem with you killing Scourged animals, of course.
This is always being debated within MMORPGs that have PvP, as some people want everyone to be able to attack, kill, and potentially 'gank' and harass anyone, while others argue that such a thing is just not fun and encourages you to be a Jerkass. The first half calls the other Care Bears, the second half prefers to call the other variations of term 'mean' and 'jerk'. Also: Griefer or Troll.
Internet Tough Guy is also getting kinda common, even if it started out meaning something different.
EVE Online has this in spades, along with appropriate Video Game Cruelty Punishment — it's not just CONCORD that'll get you either. Better ask if that innocent carebear miner has any friends before you click 'Declare War', or you may find you've just picked a fight with a guy that has friends in a very large alliance.
Though such systems often backfire horrendously — people who happen to have a lot of allies can do whatever they want to other players and call their "friends" in to support them if it goes badly.
Guild Wars used to have a reference to the "Cucco Revenge Squad" described above — normally, killing animals is fine, but there was one particular moa bird which, if killed, would cause a horde of other moa birds to appear out of nowhere and attack you.
Age Of Wushu is an open PvP world, but if you kill any "innocent" player (those minding their own business and not actively in a PvP event, like Spying, Script Stealing, Cart Escorts, etc.) you gain infamy points, which remove themselves VERY slowly, and only if you are online. Any infamy points will turn your name orange and label you as a player killer. Gain enough infamy, and your name will turn red and NPC guards and "Constable" players will come after you. If you are killed with a Red name, you're sent to jail and must remain online trapped in a small jail cell the entire time until your infamy goes back down to zero. If you manage to get your infamy so high your name becomes purple, your infamy will no longer decrease with time, and once defeated by any means, you'll be instantly sent to DEATH ROW, and have your character executed by public beheading the following day. Once executed, your character is not deleted, but respawned with a debuff that halves your stats for 24 logged-in hours. Alternatively, any player that's killed by another player has the choice, in certain situations, to place a bounty on the player who killed them, and have them confined to jail for an amount of time depending on how much the bounty was.
Conkers Bad Fur Day would eventually punish you in the multiplayer for excessive teamkilling in the form of your own teammates labelling you a traitor and attempting to kill you (at least for that life). The enemy A.I. would still want to blow your brains out, so no hiding out with them. Usually accompanied by a neat little sound clip when one of your buddies blows your brains out along the lines of "Fucking traitor!"
Bravoman featured a friendly robot at the end of each level who would give you power-ups and life-restoring food. You could punch it to net a series of funny messages like "OW! What are you doing?" and "You will regret hitting a friend". You will indeed if you do it too many times, because the robot will get pissed at you and won't show up anymore for 4-5 levels. The game is already Nintendo Hard by itself (and almost without healing items in-game), so it's not a wise choice to "hit friends"!
There's a truly bizarre variant in Mega Man Zero 2. The Crystal Cave area is full of Reploids under enemy control; you're supposed to save them, but if you kill them instead, you get a 1-up! (Maybe the life you took has been added to your own?) On the other hand, this is hell on your rank for the mission, and they won't become helpful NPCs at the Resistance Base like other Reploids you've saved.
In Lyle in Cube Sector, a couple of puzzles require you to batter around a cow and a baby bird, respectively. Don't do this more than absolutely necessary, or else they will wreak horrible revenge on you.
In the old platformer Elf, aside from ubiquitous bad guys that you have to shoot, there are also cute little animals like bunnies and ducklings. Shooting them brings up messages like "boo!" and so forth. However, shoot too many of them, and once you complete the game, the beautiful girl you were trying to save has become really ugly.
In Jak II: Renegade, you can 'accidentally' hit civilians once without repercussion, but killing them gets the Guard on your ass. Trying the same thing on wastelanders in Jak 3: Wastelander just gets you shot at and occasionally killed.
One level in Super Mario World involved crossing an entire river by jumping on top of various dolphins that can only be found in that level. In the Japanese version, you can actually let Yoshi eat the dolphins as if they were enemies. Unfortunately, doing so will prevent any of the dolphins from returning, since said dolphins cannot respawn, and therefore making the level much harder than it is supposed to. This is not present in the US version, however.
In Conquest Of The Crystal Palace, you can try to buy stuff from Kim's shop when you're low on gold. Do it too many times, however, and she'll get mad at you and throw you out.
Subverted in Ratchet & Clank: Going Commando: On Todano, there's a bus full of tourists and you can continue to slaughter as many of them as you like. The Helpdesk messages will tell you to stop and after 2 more messages escalating in intensity, a final message will tell you that you have been reported to the authorities and that you will be punished. This results in the release of an enemy — one that you are well able to handle by this point in the game, making it a slap on the wrist.
In Ninja Five-O, if you accidentally kill a hostage, you suffer half a lifebar's worth of damage.
The classic PC game trilogy God of Thunder deducts a chunk of points any time you kill an NPC (and they come back when you leave the screen anyway). The first time you do this, Odin explains and lampshades the penalty. "My son, I know it is fun to kill people..."
In Mole Mania, at various parts in the levels, Grandpa Mole will offer to fully restore your health once per screen. If you speak to him just after getting healed, he'll get a little annoyed and tell you to get going already. Keep bugging him and he'll get increasingly agitated with you, and eventually you will piss him off to the point of hostility, resulting in a instant Non-Standard Game Over.
If you want to bug him just for the heck of it and not get a Game Over, stop talking to him and leave that screen when he only responds with Visible Silence, as that is the last time you can safely annoy him.
NetHack gives characters pet dogs or cats at the start of the game. Killing your own pet has results that vary from a severe loss of luck (yes, this is a stat in the game, albeit a hidden one) to the wrath of your god, to... on rare occasion, in the case of genuinely accidental deaths, the possibility of nothing at all. (On the other hand, sacrificing your pet's corpse on a god's altar WILL piss your god off.) Eating your pet is also a very bad idea.
Likewise, cannibalism is a big no-no to non-orc or caveman characters. As well as the karma hit, the game sneakily modifies your character with a hidden ability that turns all monsters in the game from 'unreasonably aggressive' to 'horrifying unappeasable zerg swarm'. Murder of a friendly human (and only a human) carries a large penalty including loss of intrinsic telepathy if you have it. And for the biggest sin of all, murdering a friendly human being and sacrificing them to your gods? Opens a portal to hell.
Ironically, this is a good thing if you're Chaotic — then the demons summoned will be friendly, and there's a chance one of them might be a Boss from the end game, whom you now won't have to fight. The Dev Team Thinks of Everything.
The "eating a former pet's corpse is a bad idea" only applies if it's a little/large/dog or kitten/housecat/large cat, even if they weren't pets at all. You can eat your former pet giant just fine for the strength raise, but that wild and vicious housepet? Off-limits, or you're screwed.
Spelunky: Shopkeepers will fight back with shotguns if you start any trouble (shoplifting, blowing up part of their shop, hitting the damsel in a kissing booth, and so on.) In addition, for the next level all the shopkeepers will be hostile towards you, and there'll be one waiting at the exit. Luckily, they'll calm down after that level. If you kill any shopkeeper (even indrectly, say by rolling a boulder through their shop) on the other hand, every shopkeeper will be hostile towards you for the rest of the game.
Spelunky also has altars to Kali, upon which you can sacrifice live or dead creatures for favors. If you destroy one, Kali will be angered and attack with spiders. Destroying another will shackle your leg to a ball and chain, really slowing you down. Destroying yet another will cause the level to instantly go dark and summon a ghost.
Pokémon Mystery Dungeon pulls this off nicely. You can pick up items from an in-dungeon store and, even if you have no money, attempt to run off with it. Players assume that they can make it to the next floor up with their items and get away scott free, thereby making the game easier by saving money. What you then realize in short order is that the shop keeper you attacked has wicked high HP, moves twice for every one move you make, and has attacks that can KO a Lvl 100 Pokémon in a short amount of time. Assuming you survive the one (hint: you won't) there will then be a sea of them respawning for every six steps you take, meaning that you will NOT make it to the stairs. For trying to steal, you are thus beaten to a pulp and wake up (having been knocked out cold) back at your base, with half your items and ALL of your money stolen from you in retribution. The items that you retain are turned into Plain Seeds.
Though there are several ways of making it out with the loot: in the first games, by having a party member wait next to the stairs and then switching the lead to them, and in the other games by making your party wait in a safe place and using certain items that would teleport you to the stairs.
Ironically this is the only way to recruit a Pokémon of the "shopkeeper" species (albeit you need maximum recruit rate bonus just to have a 0.1% chance of getting one...) Stealing and knocking them out are fairly easy, however, with the right Pokémon and tactics (the shopkeeper species is Kecleon, by the way).
Gates to Infinity makes it harder to get away with stealing, preventing you from drawing in the items in the store with a Trawl Orb, preventing you from switching the team leader after the shopkeeper sounds the alarm, and having the reinforcements appear on top of the stairs. Warping to the stairs is still the best method of getting away with the goods, but the coast needs to be clear if you want to avoid a swift demise.
Role Playing Game
Exploring in Might and Magic 2, you can stumble across a peaceful goblin village... and choose to attack. To prove to the player that it's not always good to kill goblins, it would load as many as the game could handle.
Nice is the slightly better choice the majority of the time. Of course, there's no way to find out beforehand, and a few choices make no real difference (Nice to the innkeeper = lousy room, Snarky to the innkeeper = great room; neither affects any of your stats or future events). There are a number of cases were Snarky is obviously better in the short run, but it costs you later on (a future service is more expensive, for example). Really more a Guide Dang It than anything.
Ubiquitous in Ultima IV, a RPG and possibly the video game with the most ethical depth yet (released in 1985 - sigh.) The series is between Big Bads, and the point of the game is to develop the main character into a beacon of virtue for the people. Breaking into people's houses and taking their stuff actively distances the player from completing the game. Interestingly, this goes beyond simple cruelty to also boasting of one's accomplishments (breaking Humility), not being the last to flee a battle (breaking Valor), etc.
In the Shadowrun game released on the SNES, attacking an Innocent Bystander causes the game to punish you by taking karma points, which are needed to build up your stats. Attacking a dog will kill you (that's your totem animal).
Presumably due to a bug, you'd get the same penalty for shooting the Big Bad's corpse after you've beaten him.
Also, shooting a fellow Shadowrunner (if they aren't in your party) causes them to instantly shoot back. They don't get aggressive, they just return fire, shot for shot. Of course, they have infinite HP and you don't, so obviously it's not wise to keep shooting them... Now, the odd thing is that once you've hired them, they'll calmly stand there and take fire without retaliating, and then they'll simply respawn in whatever bar you found them in and let you hire them again.
In E.V.O.: The Search For Eden, it's possible to kill a certain friendly NPC. If you eat the meat it leaves behind (which, when eaten from enemies, is used to heal yourself and gain evo points), it instantly kills you.
This is true with all friendly NPC meat to varying degrees of penalty. This is especially frustrating in the area with giant bees carrying off baby amphibians, as it is hard not to kill them, and there is no way to differentiate bee meat from baby meat. Course it's only a piddly 7 HP compared to the whopping 999 from the elder, but when you consider your HP will still likely be in the low double digits by that point, it still hurts.
In the Neverwinter Nights module "Kingmaker," if you kill an innocent civilian, your weapon comes to life and kills you. Not surprising, considering that the weapon is actually your grandfather, a more-or-less Knight Templar paladin.
Go on. Treat your companions in Neverwinter Nights 2 like complete shit. See how many of them stick with you at the end-game.
The Elder Scrolls III: Morrowind lets you kill any character in the game. However, killing anyone plot-relevant before you get your mission from them will make the game's main storyline impossible to complete.
Supposedly, anyway. You can still beat the game... assuming you already know how. And the game does, at least, have the decency to tell you when you've rendered it unwinnable (or unwinnable without a strategy guide, at least.)
The Elder Scrolls V: Skyrim gives you to option of breaking the hearts of the many potential spouses. Once this is done, they'll never speak to you again. While this isn't too bad for some, for others (depending on who you wronged) it'll rob you of the option to sleep at an inn or buy from certain merchants. The worst, though, is if you did this to a follower; not only will they refuse to aid you anymore, they'll keep all the stuff you gave them, including the Dragon Masks.
All the games have a bounty system associated with crimes. You can do whatever you want, but if you get caught, you have to pay the consequences.
The World Ends with You plays this straight and also inverts this: at one point in the game, while you can refuse to save NPCs from "Taboo Noise", you get a minor reward for saving them. However, after you beat the game, you can replay that chapter and refuse to save anyone to find that chapter's secret item. You still have to fight one set, however (the set attacking Sota) - refusing to get involved causes Neku to start saying that he wants to move on, but then mentally slap himself and attack the Noise.
It also lampshades this with the item's hint: "Just for you, jerkface!"
Contact lets you go around and massacre random civilians if you so choose. You even get a sword that is specifically effective if you wish to do so! However, doing so makes you take massive hits to your Karma Meter, causing otherwise-friendly NPCs to attack you on sight (or, more likely, run away because they know they don't stand a chance). However, one of the possible girlfriends likes bad boys...
Killing children in Fallout 2 brands you as a Childkiller and results in bounty hunters chasing you down. Fairly well armed bounty hunters who level with you to an extent.
And then they gain lethal armor and firepower. You have to kill at least two children before you are declared a Childkiller.
Fortunately, the game doesn't care if your companions are the ones who deliver the killing blow. This is indispensable for taking out those nasty pickpockets.
In the original Fallout there are no bounty hunters, but gaining Childkiller title will make at least one town entirely hostile to you, and will make dealing with almost any civilized part of the world much more difficult. This happens even if you accidentally kill a child in the middle of nowhere and leave no witnesses.
In Fallout 3, the penalties for being a bastard remain, but if your character is too good, then the bad people you have been pissing off will put a price on your head, triggering random encounters with Talon Company mercenaries. If you disarmed the bomb in Megaton, special Talon hitmen will be summoned by Mr. Burke.
Also in Fallout 3, doing blatantly evil things, e.g. blowing up Megaton, which subtracts 1000 karma points, or Kill Satting the Citadel at the end of Broken Steel, will often close off potentially lucrative quests. If you do the latter, you stand little chance against the hordes of angry Brotherhood diaspora with heavy weapons that greet you, so you probably deserve your fate.
In Fallout: New Vegas, doing bad things to members of any of the factions will cause that faction to turn against you. While it's not such a big deal if you piss off any of the smaller towns or gangs, if you anger the more important ones, you'll get very well-armed hit squads chasing you, or worse, the entire faction becoming permanently hostile(for example, if you kill any of the NCR's high-ranking NPC's). You also lose the opportunity to recruit companions associated with those factions. Your actions with towns, minor factions, and companions also affect the game's ending.
In addition to the Regulator bounty hunters, there are also Abolitionist hitmen that spawn after you complete the Strictly Business sidequest, which involves hypnotizing and enslaving various people. Killing either of these causes you to further lose karma, resulting in a vicious cycle.
In Honest Hearts, killing or threatening (via dialogue) any of the major NPC's (such as Follows-Chalk, who you might accidentally snipe at the beginning) or being caught stealing from either the Dead Horses or Sorrows results in failure of the main quest, all tribals becoming hostile, and the initiation of an alternate quest entitled "Chaos in Zion".
The first Suikoden gives you the option to execute many of your captured enemies. Of course, with one exception (Kraze), said enemies are part of the 108 characters who must finish the game alive for the best ending. But that one execution you're allowed? So satisfying.
Especially the very talkative guy standing in the diner.
This also can help trigger the Non-Standard Game Over for this game, though this triggers by doing anything that violates the masquerade, not just actions fitting in the trope. For example, murdering people counts as a masquerade violation, but so does letting a human see you if you're playing a Nosferatu (a clan of vampires that are all physically deformed).
Less dramatically, the game inherited its tabletop parent's Karma Meter, called Humanity. A low Humanity causes it to become more and more likely your character loses control in a situation, which can easily break the Masquerade or call down a horde of cops. And one of the easiest humanity violations is simply overfeeding and killing your target.
In Spiderweb Software's Geneforge series, not only your actions, but your attitude can affect gameplay. Taking the wrong attitude in conversations with NPCs can substantially affect the way that certain NPCs and factions respond to you later in the game; changing some from favorable to neutral, to outright aggressively hostile. Getting caught attempting to steal anything from an NPC (items you aren't permitted to take are labeled as "not yours") can result in being immediately attacked and destroy your reputation with various NPCs and factions. In some cases, this can earn you an immediate Nonstandard Game Over if you anger a plot-critical NPC.
In the primitive area on Super Paper Mario, you come across Brainwashed and Crazy cavemen whom you've been sent to rescue. Killing them will actually remove points from your score (the game's EXP system.)
In Threads of Fate, the first fight against the dragon Wylaf ends when his health is halfway depleted. However, attack him beyond this point too many times, while ignoring his admonishments to drop your weapons, and he will respond by charbroiling you to a crisp in a cutscene. Needless to say, this is an instant Game Over.
If you choose the Dark Side path in the first Knights of the Old Republic, more than half the crew would turn on you, forcing you to kill them. A cut ending specifically for Dark Sided females added an additional twist to turn it into an Everybody Dies ending by having Carth show up and making a final appeal. The player could then turn on Bastila, allowing the Republic fleet to destroy the Star Forge, with Revan and Carth still aboard.
In Baldur's Gate, if you go around slaughtering civilians, a squad of Flaming Fist mercenaries shows up to slaughter you. They're nearly impossible for a character at your level to kill, and even if you do manage to beat them, more will keep showing up later on.
Additionally, in this one and the sequel, getting caught pickpocketing, killing NPCs, or summoning something that kills NPCs activates a toned-down version of Everything Trying to Kill You.
Baldur's Gate and its sequel are deeply unfriendly to evil characters. If you take the 'evil' option in a given quest, expect to receive a smaller reward or no reward at all. If you allow your reputation to fall into the ranges where your evil-aligned companions start complimenting you, expect prices to shoot through the roof and (at extremes) your good-aligned companions to abandon you. All of this is in addition to the above mentioned swarms of infinitely respawning guards when you let your reputation fall too low. And to add to the injury, you only have four evil-aligned characters (one only appears in the expansion), so get used to a non-full party, or squeeze in some Token Good Teammate who is at best Chaotic Neutral.
On the other hand, Edwin, Viconia, and Korgan/Sarevok are arguably the most powerful of their respective classes...
Dragon Age: Origins, while lacking a Karma Meter, has a few points where making an obviously evil choice causes allies to abandon you, regardless of their disposition towards you. Cruel actions will also earn you the disapproval of certain companions.
Acting like a dick in the Dalish camp, either by breaking up a pair of young sweethearts, mocking a grieving widower, or trying to loot a chest after Lanaya asked you not to, results in the local smith refusing to trade with you. Since he has an unlimited supply of elfroot — one of the components in healing poultices — this is a poor choice.
Pickpocketing in Denerim will end up with you getting a small army of guards attacking you while traveling through the city, complete with the guards mocking the "mighty Grey Wardens" for stooping so low as petty theft.
Completely inverted in the case of Owen, Redcliff's blacksmith. You can simply kill him yourself or tell him that his daughter, who was missing, is dead, after which he hangs himself. Your "punishment"? A replacement blacksmith that sells the best bow in the game. You can even lie to said replacement blacksmith and tell him that you knew Owen very well, netting you an amulet originally belonging to Owen's daughter. Who may still be alive and even make it safely back to the smithy, depending on your actions.
Choosing the Closed Fist option near the end of Jade Empire results in your more morally upstanding party members turning on you. If you succeed in killing them, they're (obviously) unavailable for the rest of the game.
That's not the real punishment, though. That comes if you abuse the Plume, in which case Freya gets wise to your antics and drops down from the heavens to kick your ass.
Fable II has a few choices in storyline wherein you get to choose an evil option (generally going around killing people) and a good option (which is usually going around killing people, just evil ones). The evil option, such as working for the Temple of Shadows or killing a farmer or electing not to help Barnum, will ultimately create a more unpleasant world, which, of course, means less game options.
A lesser example involves NPCs. Kill someone to buy their house at a lower price, and you'll end up making less money than if you just bought it fair and square.
Persona 4 actually tries to induce Video Game Cruelty Potential with Nanako, your adorable cousin, with her "I love you, Big Bro!" Squee! Then of course, she is kidnapped by Namatame and taken into the TV world. After you rescue her, she apparently dies. The punishment comes from the fact that even though you really, REALLY want to, pushing Namatame into the TV (or failing to convince your teammates that there's something you're missing) nets you the bad ending. And a Kick the Dog, since he's not really the culprit.
In both Persona 3 and Persona 4, while the player is given the option to be complete assholes during Social Links, it's pretty much never a good idea; breaking relationships will inhibit your progress in the dungeons since the Relationship Values have a major impact on the development of your Personae. If you try to play the character as an anti-social Jerkass, chances are you won't get far.
This is before getting into trying to cheat on your current love interest in Persona 3.
Yume Nikki and most of the fangames associated with it gives you some kind of killing implement to use as you desire. But try using them on the wrong NPC or the Goddamn Bats and you'll probably find yourself screwed over in some manner. Some might even be Demonic Spiders in disguise who proceed to outrun you, forcing you back to the nexus.
.Flow in particular has a rather brutal punishment for trying to beat one of the local Goddamn Bats over the head while he's drinking: Countering your attack and then outright killing you in retaliation, which forces you out of your trance, but not before a short cutscene showing Sabitsuki's decapitated and busted up corpse. Also, in general, it seems that angering one will anger the rest while you're still zoned in, and one in particular happens to be a Demonic Spider...
Demons Souls took punishment to the extreme. If the player, whether intentionally or not, attacks an NPC, the NPC will continue to fight you until you kill them (if you die, the NPC will continue to attack you after you respawn). If you kill the NPC, he/she will never come back. This is true even if the story cannot be continued without that NPC. Considering that there are no save points, or any other way to "undo" the damage, this can be literally game breaking. Especially cruel given the length of the game.
Luckily, most NPCs don't aggro with one hit — you usually have to strike them multiple times before they get pissed off.
The Maiden in Black and Monumental seem to be the only ones needed to finish the game, and they either revive or are immortal. Deaths of other characters will deny you services, but are endurable.
In Mass Effect 2, you can choose to help either the Justicar Samara or her sociopathic Ardat-Yakshi daughter Morinth during their Mexican Standoff. Helping one means the other dies. If the player chooses Morinth, not only are they deprived of a war asset and one of the most poignant scenes in Mass Effect 3, but they also have to fight Morinth during the game's final stage after she's been turned into a banshee by the Reapers (and she makes no other appearances during the game). In addition, being a literal Black Widow doesn't stop Morinth from trying to sleep with you in the second game, and if you do, it goes exactly likeyou'd expect.
In TaskMaker, killing any NPC with a Good alignment reduces your Spirit and knocks your points way down. Kill the "Mom" NPC in Enitsirhc, and your player is permanently rendered blind, deaf, and drunk (also making it impossible to continue).
Shoot Em Up
In Star Fox, if you shoot any blue stingrays in Sector Y, they ram you. If you avoid them all and shoot all the yellow stingrays, you get the Space Whale bonus.
Also, shooting your own teammates will make you not have as much backup in the next mission. Though to some, they would rather have no backup due to the backup always requesting backup. In 64, however, you can't collect the medal for a level if any teammates are grounded.
In Raiden Fighters, you can uncover fairies that, when collected, yield 100,000 points each. You can also shoot them, and if you shoot a fairy enough, she will die, resulting in a "KILLED THE FAIRY!" message and a mere 10-point bonus; that's 99,990 points lost. It's very easy to do by accident.
In most Escape Velocity games, boarding and capturing enemy and civilian ships is a good way to earn extra cash or get escorts. Do that in the Starfleet Adventures mod, and you'll be court-martialed and thrown out of Starfleet.
Trauma Center. Whoo, we have a tough case here. From what you can see, your job is to fight some strange malicious virus that's somehow looks like a vector graphic version of aliens from Space Invaders. But here's the thing: that's the only thing you'll be killing through the whole game(s). You can try hurting the patients you're treating, but it will only result in a bad rating for your stage. Oh, and Angie and Val will scowl you pretty badly, which is something you will not want these two cuties to do. At some point of the game, you may realize that this series just... leaves no room for cruelty!
On the other hand, if you wanted to get higher scores, you had to let the viruses wreak havoc inside your patients, so you could rack up points treating the lesions, wait until the viruses attack again, rinse and repeat for higher and higher scores. Instead of, you know, killing the viruses. So it's a mixed bag.
The first Wing Commander game allowed you to kill your wingman without retribution. Later games made the wingmen start fighting back if it was obvious you were trying to nail them, and WC3, possibly others, had you get court-martialed if you returned to base after shooting down your wingman. Unless you ejected after the deed, in which case the game forgot that you did the killing.
In Harvest Moon DS, if your animal dies for any reason (even old age), then your friendship with the townspeople drops a lot. To make it even more interesting, killing animals is required to marry the Witch Princess.
The games also allow you to give nasty things to the townspeople, like weeds or bugs. Their friendship meters drop accordingly. Do this to much to your wife or husband and (s)he'll divorce your sorry ass.
Try raising or gathering poisonous toadstools and throwing them into the community pot at the Harvest Festival. Low-level toadstools result in sharp friendship drops with all villagers (except the Witch Princess, who presumably found it hilarious and is never invited, anyways). A level 100 toadstool... credit roll.
Animal Parade makes it so townspeople actually register when you use your tools on them. Swing your axe, hoe, or even your watering can at them, and watch them hate you in record time.
In A Wonderful Life, neglecting your farm in the second year and beyond and then acting rudely to your wife when she questions you about it will cause your wife to take your child and leave you forever. It's nearly impossible to do this by accident, though; you basically have to be trying to get this ending.
Also in this game, if you max out Celia's heart points and marry another girl, her homestead will never forgive you.
Rune Factory Frontier, a spinoff of the HM series, does exactly this. If you attempt to cheat on your wife after marriage by trying to marry another bachelorette, after eliciting a "What the hell, Raguna?" from the bachelorette, your wife will storm angrily down to the date and beat your ASS. You're left with 1HP and 0RP (Essentially writing that day off in terms of workability, unless you have a stock of HP/RP replenishing food items, since the baths are closed on holidays/date days) and more importantly your wife's Friendship and Love point values reset to zero. Given that this is a game where you have to really work hard at getting your potential love interest to like you, this is a pretty huge blow, and devastating if you've married Bianca, Cinnamon, or Selphy as they all have pretty difficult to find or craft items. (Or in Bianca's case, can only be increased by constant attention.)
In Rune Factory 3, a similar situation to A Wonderful Life occurs if you woo Raven and don't marry her. She writes about it in her diary. What makes it worse is you do this after she pours out to you that she's afraid she will be alone forever
Ace Combat Zero: The Belkan War allows you to indulge your Video Game Cruelty Potential by taking out civilian or damaged/disabled military targets. However, doing so sets you on the "Mercenary" part of the Karma Meter, leading to harder enemy ace squadrons going after you.
Subverted in that depending on gameplay variables (namely player ability and plane), they may not be that much more difficult than the "Soldier" or "Knight" squadrons that you encounter on those mission versions, and by moderating the ratio or by playing Free Mission (only the Campaign affects the Ace Style Gauge), you can avoid the Mercenary missions altogether, since your position on the gauge at the end of a mission determines the next mission's version.
In the PC version of Star Trek: Starfleet Academy, firing on any Federation starbase would cause the mission to instantly abort, whereupon the instructor brands you "childish" and makes you restart the mission.
In SimCity 2000, churches randomly appear in residential areas. Unfortunately, they can be a bit of an annoyance, as they don't contribute taxes to your budget. It's possible to bulldoze them, but when you do, two more will appear in other residential areas. This can continue until your entire residential area is filled with churches, which will give you no taxes whatsoever.
In the original SimCity, bulldozing churches would kick-start a disaster.
Which is ironic as the creator is an atheist.
An atheist who believes churches to be the worst thing he could inflict on you.
Lets not forget the wonderous "church virus" code. Type any curse word into the game and you'll receive a message stating "same to you, buddy!" and churches start appearing at alarming rates.
You can do pretty much whatever you want with adult Sims in the series of the same name, but if you neglect your infants or toddlers, the social worker will show up to place your child in a foster home. The same is true of housepets in the Pets expansion, so think twice before you Kick the Dog.
In F/A-18 Hornet, if you hit any allies or friendly buildings, you get a Nonstandard Game Over where you are "court martialed".
In Novalogic's F-22 games, there is usually a mission where you are part of the force escorting Air Force One. Normally, when you acquire a target, it's designated enemies only. When you highlight your friendlies with your radar, they don't mind. However, even HIGHLIGHT, let alone shoot at Air Force One, and all 30+ escort planes will shoot your ass down — in addition to any friendly SAMs around.
FreeSpace gives you some leeway if you hit your allies in battle. But if you start to cause more damage to your wingmen or escort ships than the enemies, they call you out on it. If you keep poking them with lasers, all friendly units in the mission turn hostile and attack you.
Thankfully, you can just sit there until the rebel mentions how he knew all along, and your mission becomes "Protect the transport" after your cover's blown.
Not to mention that if you do blow up the transport, the rebel still reveals that he knows you're a spy, and calls you a heartless murderer before turning on you anyway.
You don't even need to do that, depending on the version. As the leader is waiting for you to open fire... Take a Third Option; fire at him. A quick and lucky pilot can frag at least one rebel, maybe two or even three of them. Then you just need to dance with them a bit until The Cavalry arrives.
Likewise, while letting tigers or T. rexes out of their cages to chase guests in Zoo Tycoon can be amusing, it'll also deep-six your zoo's rating.
In Vietcong, killing a montagnard will result in mission failure.
Hitting villagers with your net or axe in the Animal Crossing games will cause them to become extremely angry or sad, preventing you from talking to them until their mood gets better and drastically lowering their disposition towards you. Eventually they'll move out altogether. (Though depending on how much you like the villager, this could be a good thing.) Other actions which will lower villagers' disposition towards you and probably make you feel bad: denying them medicine when they're sick, giving them a bug or rotten fruit when they ask for fruit, pushing them around.
The sequel doesn't make you lose synchronization, but instead sticks with the "kill three and you lose" rule.
This inadvertently nullifies the Video Game Cruelty Punishment, as the player can simply kill two civilians, and then wait a while for the effect to reset, or kill a guard to have it reset immediately. This means that the player could kill the annoying civilians who harass you during missions with no penalty.
In Metal Gear Solid 2, if you go around shooting seagulls or doing sinister things in the women's bathrooms, then your CO calls you a monster, your girlfriend breaks up with you, and you can't save until you've said sorry.
In Metal Gear Solid 3, the more soldiers you kill, the harder your encounter with The Sorrow becomes.
Likewise, if you go on a major killing spree in Metal Gear Solid 4, you collapse to the ground and throw up from the gore. All while the villain's mocking voice echoes in your head.
Killing children in Metal Gear 2 reduces Snake's life gauge. Given what most of the punishments entail when killing anyone, this is surprisingly lenient.
Metal Gear on the NES and MSX allows the character to shoot hostages. All of these except The Mole reduce Snake's rank, which translates to lowered health and ammo capacity.
This can actually make the game Unwinnable, since you need to be at top rank to gain access to certain radio contacts, who will then leave vital weapons and equipment for you to pick up. Certain hostages are also related to said contacts, and killing them breaks off their contact with you, also making the game unwinnable.
In the first two Splinter Cell games, killing a civilian or other innocent would cause you to immediately fail the mission. This was averted in Splinter Cell 3, where you could massacre whoever you wanted (including civilians and even U.S. National Guard soldiers) and the mission would still continue on as normal (although Mission Control will berate you for going Ax-Crazy, and you receive a 0% score at the end). In Splinter Cell 4, killing civilians and security guards affected your Karma Meter, which (if you did it a lot) could get you a Bad Ending or even a mission failure.
Dishonored doesn't really go for overt punishments (unless you break the plot by killing an essential character, anyways), and it certainly is possible to go through the game wantonly murdering every single enemy you come across. Doing this leads to a high Chaos rating, which means more rats, Weepers, and security systems to contend with, plus the overall story becoming much darker. The game is also surprisingly good at guilt-tripping you if you take the "indiscriminate slaughter" route.
In Eternal Darkness, killing innocent people takes away a big chunk of your sanity meter (and when your Sanity runs out, your Health). When this meter empties, strange and terrible things start to happen. Depending on the player, though, this might be an incentive to kill every civilian you come across.
In some places, particularly Maximillian's chapter, there are entirely normal human servants milling around the house, tending to various things. Some of them are actually bonethieves, monsters who burrow into human bodies and control them from within but don't change their outward appearance. Later in the chapter, when they start attacking you, it's easy to tell them apart, but if the player tries to make things easier on themselves by killing the bonethieves as a preventative measure, that sanity goes down real fast.
What's worse is that when your sanity is low enough, talking to people will also yield different descriptions. For example, in Peter Jacob's chapter, it's possible to save a woman from a bonethief, but talking to her will still create the impression that she's a monster. Killing her, of course, still lowers your sanity meter. It's probably the scariest sanity effect in the game.
The Suffering will inflict more and more screamers and scares on an evil player who shoots everyone he comes across, rather than helping (or at least trying to help).
During the "cabin defence" sequence in Resident Evil 4, if you shoot Luis (who spends good part of the level handing you medicines and flashbangs that only hurt Ganados) too much, he will (quite understandably) turn on you and kill you in a cutscene.
It's entirely possible to have literally every faction except the Loners and the Scientists (both of whom more or less stop showing up late in the game) pissed off at you in STALKER: Shadow of Chernobyl. Why in hell you would deliberately do this is a mystery.
In most The World of Darkness games, all characters have a stat that tracks how moral they are; it's generally a good idea to keep this stat high. Vampires who are low on Humanity are more prone to frenzy, where you go on a brief uncontrollable rampage, in a setting where keeping a low profile is important. It also increases the length of torpor. They also have trouble interacting with regular mortals, as their Uncanny Valley nature starts to come to the forefront. Stooping to any atrocity will eventually drop your Humanity score to zero, which reduces the character to a mindless beast which is no longer suitable for play.
Beyond that, certain acts are so nasty that the games have special rules built to ensure violators are punished, especially in the Old World of Darkness; committing them results in instant loss of Karma Meter. The major one in both settings is diablerie, a vampire eating another vampire's soul to steal his power. In the New World of Darkness gameline Promethean: The Created, committing lacuna (stealing another Promethean's vitriol, a form of Experience Points gained by completing milestones — or in other words, sabotaging another Promethean's Pilgrimage for petty gain) is another instant-punishment act.
Other New World of Darkness games: For werewolves, low Harmony increases the number of triggers for Death Frenzy and makes dealing with spirits harder; for mages, low Wisdom increases the power of Paradox, which as well as the inherent problems, can lead to them being targeted by fellow mages; Sin-Eaters with low Synergy find interacting with ghosts and performing ceremonies harder, as well as having their own Geist make more and more unreasonable demands and eventually start possessing them; and for Changelings, low Clarity results in muddled perception (as you can't tell what's real and what's fantasy), causes them to be ostracised by their peers, and makes them a bigger target for the True Fae. ... And, when coupled with high Wyrd, begins to turn them into one of the True Fae.
The Old World of Darkness game Changeling The Dreaming had Banality and Bedlam for players to worry about. Too much Banality - which, if you weren't careful, could be very easy to pick up and was kind of difficult to shed - and the Changeling would forget who they were, at least until they got an infusion of glamor (assuming it was early-stage Banality; late stages might leave the Changeling so drained of glamor that they wouldn't ever remember anything about magic or who they really were). Bedlam, on the other hand, was caused by spending too much time away from normal, mundane things and was actually more dangerous since it caused the person to become disconnected from reality of any sort. First-stage Bedlam could easily be self-medicated by wandering off to go steep in low levels of Banality for a while, but second and third-stage Bedlam were actively dangerous since they were much more difficult to treat and cure (third-stage Bedlam was, in fact, impossible to cure) and the delusions could lead to the character doing anything from trying to hug a dangerous monster, or attacking their allies, to — using an example from the Nocker Kithbook - experimenting with Banality and then unleashing your experiments on a whole city of Changelings. The whole thing was designed to emphasize how Changelings were really stuck between the two worlds — too magical to live in the human world, too human to live in the Dreaming.
Meanwhile, over in Fan WorkGenius The Transgression, low Obligation leads to trouble interacting with Muggles. Which gets to be a bit of a problem when you consider that you need human contact to keep said Karma Meter up. Oh, and that mad science tends to be expensive, so if you can't hold down a day job, no death rays for you.
Cthulhu Tech essentially runs on this trope; killing innocents, even unintentionally, ranks up with reading the unabridged Necronomicon on dinging the sanity meter. Being responsible for a massacre beats everything but seeing Cthulhu himself when it comes to driving player characters crazy.
This is due to the fact that humanity is almost completely united under the New Earth Government, their numbers have been devastated, and they're under constant threat of extinction by alien forces. Each non-crazy human is a precious thing under those circumstances.
There was an expansion to the pen and paper RPG, featuring a lunar colony after the enslavement of Earth by the Elder Gods. It featured a sanity loss score for "knowingly and willingly causing the extinction of the human race." That was the second highest possible sanity loss.
Earlier editions of Dungeons & Dragons had the Paladin's code of conduct, which kept him acting in a Lawful Good manner and not randomly slaughtering people. Breaking the code would result in the paladin losing his powers until he atoned for his wrongdoing. Of course, this was all too easy to abuse by jackass DMs who would try to railroad the paladin into a situation where he must violate the code.
Certain other classes, such as Clerics, also had their powers depend on a code of conduct, but these tended not to be enforced as strictly as the Paladin's.
The Game Master might also implement other measures to keep psycho PCs in check, such as changing their Character Alignment to suit their actual Stupid Evil style of play, or sending the local authorities after them. This is also one of the reasons why no sane DM would award experience points for killing civilian or "friendly" targets.
The best response to rampaging PCs is to realize that 1) they are not the only adventurers in the world, 2) someone whom they have wronged can spend a lot of money to hire those willing to revenge the wrongs, 3) there are always adventurers, good aligned churches, orders of paladins, noble-minded wizards, and so on willing to respond to murderous bastards who are to quick to butcher innocent people, and 4) spells like Speak With Dead and Clairvoyance can make identifying the culprits rather easy. Good GMs make the punishment seem to come organically from the game world without needing to use game mechanics.
Dead Inside has this as part of the whole point of the game. The game is designed specifically to discourage the usual Tabletop RPG standard of "kill them all and take their stuff." The PCs are (by default assumption) people who for various reasons lack most of their souls. Doing bad stuff (especially killing people) can result in losing the rest of your soul and becoming one of The Heartless. Conversely, doing good things, helping people, being courageous and optimistic, and whatnot helps regenerate soul-energy, which can be forged into a new, complete soul, which is pretty much the default goal of the game.
After that, though, things get a lot more complicated, as you're now on the radar of more than a few ruthless, Machiavellian bastards who just stole enough soul energy to outpace soul decay, and they've got a lot of practice at taking advantage of others. Meanwhile, you've got a big sign on your back that says, "Steal this new soul from me before I become a rival." You can still do well being a good person, but you're now at a point where being Good Is Dumb is dangerous and being cleverly cruel to get around punishment starts looking more attractive.
Built into the system of Dark Heresy, where especially cruel and immoral actions (and keep in mind this is cruel and immoral by Dark Heresy's standards; we're in 'wanton slaughter of innocents For the Evulz' or Deal with the Devil territory) grants you Corruption Points. Corruption Points give your characters derangements and physical defects, makes you more vulnerable to the lure of Chaos, makes puritans more liable to burn you at the stake, and ultimately renders the characters unplayable.
Of course, this being Dark Heresy, there are a number of other ways to get Corruption Points unintentionally as well; odds are 95% of Corruption Points will come about as a result of failing Will Saves or similar (such as being a Psyker) unintentionally. Being cruel and evil on top of that just adds a lot of grease to the ol' slippery slope.
Third Person Shooter
In the tutorial level of Second Sight, there is one room that contains an Assault Rifle in contrast to the training weapons that you are supposed to use. You can pick the gun up and start shooting people, but then they'll send everyone after to take you down. Then you'll get lectured by The Voice.
In any of the level where you have a partner, you can shoot them to death yourself and they won't fire back. But the level instantly ends and you are once again lectured by The Voice. You get the same effect if you leave them to die, just with a different speech.
Mega Man Legends allows you to give into your dark side and just be a total jerk. Kick trash behind the store counters in the mall. Insult a painter by saying she has no talent. Kick puppies. Foil a bank robbery and then run off with the money. Volnutt will slowly turn black the more he does this, and stealing the money for yourself permanently turns you black and prevents you from acquiring certain power ups and NPC interactions later on. Doing the right thing of returning the money would later reward you with more money than the amount of money stolen from the bank anyway, so it's really not worth it.
To a lesser and more immediate extent, if Roll is with you on Mega Man Legends 2 and you try to Use the grabber on her, she slaps you, actually causing damage.
Inverted in Spec Ops: The Line: executions (which become increasingly brutal and vicious as the game wears on) reward the player with more ammunition. Granted, given the context of the game, it doesn't really feel like a reward.
Turn Based Strategy
In Disgaea, you are given the option of sacrificing (or accidentally killing) your own allies on the battlefield. However, the good ending will be barred from you if you kill even one of them. If you kill certain numbers of allies and then kill certain bosses, you run the risk of having the other main characters of the game grow tired of you and try to overthrow you.
Having 99+ Ally kills is one of the requirements for the WORST ending of Disgaea 2.
In Soul Nomad & the World Eaters, you can use Gig edicts to steal from, pick fights with, steal stats from, and in many other ways royally mess up the populace of Haephnes. However, if you try to attack people who obviously cannot fight back (like old ladies, babies, birdfeeders, and posters), a level 30 character known as 'Heroman' will appear and fight you in their place. Heroman belongs to the Game Breaker class known as the 'gideon' that can mutilate just about anything else in the game (and Revya and any unit he/she leads is the worst matchup possible against one), and levels up 10 levels every time you defeat him.
In Jagged Alliance 2, killing your mercs intentionally by having them attack each other or blow themselves up will discourage new mercs from joining you and prevent you from collecting their life insurance.
Killing civilians, on the other hand, reduces the towns' Loyalty score, making it harder to train militia in their defense. Well, except for the hillbilly survivalists, but they don't really count as "civilians", since they'll start peppering your squad with shotgun shells the moment you step out of line... (by, for example, trying to loot the locked boxes in their shed.)
Xenonauts: In an apparent attempt to dissuade veteran X-COM players from applying the usual "level everything in sight" tactics, you suffer a rating penalty if civilians get caught in the collateral damage.
Speaking of X-COM, if you charge right into indescriminate slaughter on terror missions, you'll quickly find that you lose a lot more rating points for killing civilians yourself, than you would if they get killed by the aliens. The same applies to killing your own soldiers. And if, god forbid, you completely ignore a terror site, you get minus 1000 rating points, in a game where getting 500 positive points per month is a lot.
Tokimeki Check-In allows you to rape one of the female leads, but doing so gives you an immediate Bad End. In two separate instances, you can watch her get raped without intervening, and while you get away with this, it has repercussions. In the first instance, you won't be able to progress her plotline thereafter (although you can pursue another girl's plotline), and in the second instance you won't be able to progress the plotline of the girls who raped her (Ayame's already lost to you at this point, even if she wasn't raped the first time).
Three Sisters Story will punish you for sleeping with more than one of the titular sisters, or for sleeping with any other girl in the game without a condom. Moreover, if you rape one of the girls instead of letting her admit that she's a lesbian, she'll kill herself in front of you.
In Glo-Ri-A, you can rape a character in the prologue, but afterwards she shoots the main character dead, and the player gets an admonition to "Play More Serious!"
Episode 2, if you choose to consult Helen, have the option to allow her to punch Yale, and even punch Ted, just in case you are feeling suicidal.
Episode 8, similarly, allows you to punch Duke in the nose. This obviously results in a Game Over, but it's worth it to see Frank tell him to not be such a pussy.
Wide Open Sandbox
Bully gets this way too. Even if no law enforcement is around, start attacking 'protected' targets (adults, girls, little kids) and they will spawn (not run in, spawn) and chase you.
And if you are caught too many times, you are given detention and forced to do a short minigame.
Grand Theft Auto. Start killing a bunch of civilians and the police will try to kill you, getting more and more aggressive as your wanted level increases, causing them to come after you with armored cars, helicopters, and eventually military tanks. Killing cops or any other person of law enforcement shoots up your wanted meter tons faster than killing innocent people.
In Grand Theft Auto: Liberty City Stories, the cops were much more aggressive, with fast police cars (often four at a time) that would ram you constantly, spike strips every ten seconds, and deliberate aiming at the tires (which greatly decreased your car's performance). If any cop managed to get next to your vehicle door, you were insta-busted.
In Spore, using Gravitation Wave, Fanatical Frenzy, or a Planet Buster will cause nearby space-faring races to go hostile with you, except the Grox, who will become more friendly toward you.
Allying with the Grox will make everyone in the entire galaxy hate younote Specifically, it adds a -200 relation modifier to every empire, even those you uplift later or have never met. Under normal conditions, this is enough for them to declare war, which requires a net bonus of -75. This includes your allies unless you've been spoiling them(If you just want them to not declare war, you need a minimum of +125 at the time you ally the Grox. If you want them to remain your ally, you need a minimum of +225) — all at the same time!
In Crackdown, you will immediately draw aggro (and a lot of gunfire) from Peacekeepers (police) if you shoot them or any civilians. Hitting them with your car reduces your Driving stat. It's entirely possible to have the cops and the gangsters pissed at you at the same time.
In fact, one particular racing mission specifically requires the player to drive at top speed through an artificially congested area, making it impossible not to run over pedestrians or Peacekeepers, at which point the game spawns far more Peacekeepers than usual. The point of the race then becomes surviving long enough to get to the final checkpoint.
In inFAMOUS, you have six Karma Ranks, three for Good and three for Evil. If you get the third Evil rank, Infamous, the pedestrians may suddenly decide to attack you by either punching and kicking, or throwing rocks at you.
On the flipside, if you decide to give into your more saintly ways and get your karma all the way up the good alignment, the thrown rocks will suddenly be striking your enemies instead, not to mention you'll have more opportunities to gain more experience and be tipped off to enemy ambushes.
Elite lets you blow up friendly ships and even steal their cargo from the wreckage. However, such acts of piracy earn you a legal status of "Fugitive", which means that every police ship and bounty hunter in the game will attack you on sight. And attacking a Space Station is near suicidal, as you will quickly find yourself facing the planet's entire fleet of police vessels.
In The Godfather: The Game, getting your Heat up too high by killing too many civilians, policemen, or security guards would instantly negate the temporary immunity from police attention that you could bribe a Dirty Cop into giving. Kill enough gangsters from one Family and you could max your Vendetta, starting a Mob War. Abuse a shopkeeper or racket boss too much and they would fight back, so you couldn't get them to switch to the Corleone side for a while. If you kill one of your shopkeepers or racket bosses, you would lose the income from them for a while.
Killing civilians in Mercenaries costs you money and makes every faction (except The Mafiya in the first game) think less of you. Of course, if one activates God Mode, they can simply run around destroying everything until they're broke.
Then there is the fact you can destroy any building in the game in the sequel; however, destroy a Faction's main building and all your favoring with them instantly turns hostile.
Red Dead Redemption has a potentially frustrating "mission" that requires you to take your cows out to pasture. Along the way, some of these cows will wander off, or get stuck on rocks and trees and just will not return to the herd. This obviously becomes frustrating, and you may want to take it out on the cow in question by putting a slug between its eyes. However, even though you OWN the cows and have 14 other ones in the herd, the game fails you for bringing any harm to them whatsoever.
The game is also protective of its corn, but that is another story...
Cruelty to innocent people in general will usually have consequences. Those bounties can be a bit annoying.
Also, killing any of your family members will cause the game to instantly end and restart at the last save point.
Terraria is usually very tolerant of your evil ways, allowing you to slice bunnies and birds in half left and right. There's even a voodoo doll that lets you kill one of the NPCs at your will! Throw that voodoo doll into lava, however, and you get attacked by the massive Wall Of Flesh. It will rip newer players apart, and there is literally no escape — you HAVE to kill it or die to escape.
This is actually an important part of the game, as you have the beat the Wall of Flesh to advance into Hard Mode and spawn all the REALLY cool stuff. It's not so much an optional cruelty punishment as a major challenge.
In Minecraft, hunting wild animals for supplies and defending yourself from hostile monsters has no penalty (and indeed is just sensible gameplay). However, wolves and zombie pigmen only become hostile if attacked. Since they spawn in groups, attacking one leads to the whole family coming after you. There's no bad effects to be had from attacking or even killing tamed animals, though, unless you count losing the benefits they provide in the first place.
Killing Villagers in villages will also alert Iron golems (probably built by the villagers as guardians) to attack you.
Don't Starve averts this Minecraft solution. Every animal (non-hostile) has its innocence level measured in numbers. If you fill it to 30 (for comparison, the worst is killing a butterfly, yielding 6 points), Krampus will spawn and rob your chests. And if you surround your chests with Bee Mines, he'll blow himself up, giving you the most efficient storage backpack in the game.
In Red Faction Guerrilla, each civilian you kill costs you one point of sector morale. This has almost no gameplay effect, but it's annoying — and since the Red Faction is basically a terrorist group, sparing civilians can be very tricky.
Other / Unsorted
It's not a part of the code, but when you kill people without reason in Mitadake High, they will label you an RKer (random killer) and you are either banned from that server or so very dead.
In Sabres Of Infinity, bloodthirsty behaviour that violates the rules of engagement (such as killing civilians and executing prisoners) will damage your reputation. Ignoring your men's needs and/or being excessively harsh towards them may cause them to rebel against you or undermine their combat effectiveness.
In Judge Dredd: Dredd Versus Death, killing random civilians loses you points for the level. Lose enough points and the Special Judiciary Service ("Who watches the Watchmen? We do.") turn up to gun you down.
Amusingly, they show up in places they shouldn't even have access to, including the final mission on Deadworld, an evil alternate universe populated by the undead.
In Half-Minute Hero, if you try to short-change the Time Goddess in "Hero 30", she takes away all of your equipment after a set time, making it near impossible to clear the level.
In Madden NFL, if you attempt to run up the score to a ludicrous degree (hundreds of points, which is possible with low difficulty and money plays), the game will flash a warning begging you to stop scoring or else you'll "break the game."
In the NCAA Football series, there is an actual penalty for doing so: you will lose sportsmanship points if you do things considered unsporting, like running up the score or going for it on fourth down instead of punting when you have the lead.
If you shoot your teammate in the Midway arcade game Vindicators (or its "Midway Arcade Treasures" version), your fuel and points will be transferred to them with each hit, until you die. (This can actually be a legitimate tactic to help your partner out.)
Shooting innocent cars in Spy Hunter costs you points (specifically, it blocks you from scoring for a period of time, and under normal circumstances, merely driving increases the score). In the 3D games, you fail the mission if you kill too many.
In the Light Gun Game / Rail Shooter part of Die Hard Trilogy, if you kill any cops or SWAT officers, the game will display the message "Major Disaster" and they will turn against you.
In Paperboy, if you damage a customer's house, they will cancel their subscription. If you lose enough customers, it gives you a Non-Standard Game Over screen with the words "Paperboy Fired".
The mobile card game Ayakashi: Ghost Guild punishes you for attempting to attack other players that are ten levels or more below your own, counting it as a loss on your record and taking away some of your silver (currency needed to raise the level of your cards through fusion).
In the first Homeworld you can attack the Bentusi. At first, they ask you to stop, but if you don't, they wipe you out.
Eridan in Homestuck, in the Land of Wrath and Angels, took it upon himself to kill all the angels. Despite the fact that they did not drop Grist, indicating that rather than enemies, the angels were the innocent citizens of the world (like the salamanders in the Land of Wind and Shade, or the crocodiles in the Land of Heat and Clockwork). The angels, which only died after minutes of sustained fire from Eridan's high-level weapon, proceeded to swarm him at all times once he began killing them (much like the classic chickens in The Legend of Zelda).
In Sonic the Hedgehog 2: Special Edition, if the player mistreats Tails, he will retaliate. Docfuture does this by abandoning Tails in Casino Night Zone, so Tails starts using the game's hint mode to dish out passive-agressive mockery. Eventually it escalates to the point of Tails trying to kill Docfuture (though this is eventually revealed to be the result of brainwashing).