Not only can you kill all the main characters in Heavy Rain in a variety of cruel ways, one of Ethan's trials requires him to cut off his finger. You can get him drunk to ease the pain, grab a piece of wood to put between his teeth, and sterilize his finger...or you can skip all of those and grab the saw.
If you grab the saw or the scissors, you have to do another QTE to hack the rest of it off.
It's also possible to arrange things so that all the good guys die, The Bad Guy Wins, and all possible evidence that could implicate him is gone, allowing him to get off scot-free. You even get an achievement for it!
In Epic Mickey, you can melt not only bad guys, but friends as well. You can dump Oswald's children into a bunny pool. You can turn blotlings into friends and then knock them into a pool of thinner. The game even has a Karma Meter throughout the entire thing.
The clock tower in the small world attraction? You can destroy that too.
Petetronic? Turn him into the MCP. Hook? Throw him into an animatronic Tick Tock the crocodile. Mad Doctor? Uh, both ways, you destroy his machine and send him flying. Shadow Blot? Thin him out. The actual Phantom Blot? LAUNCH FIREWORKS AT 'IM!
Early in the game, you have to choose between saving a Gremlin or catapulting him away for some E-tickets.
Gus: Mickey! You chose E-Tickets over the safety of a Gremlin! You launched him to who knows where! You are supposed to be the hero! You are the hero, right... Are you?
You get the chance to do it again in the sequel, with a pin for it. We know he's fine this time, though. You can also go around shocking everyone with Oswald's remote or blowing up fireworks next to them.
Tip: The Legend of Zelda: Link's Awakening chickens are vulnerable to magic powder and fire. Time for revenge! This works on the dogs in that game as well. That's right: you can immolate your neighbors' pet dogs.
In The Legend of Zelda: Ocarina of Time, you can ride your horse over the chickens on Lon Lon Ranch. Since you couldn't be damaged while on horseback, a flock of chickens would fly behind you waiting for you to get off.
Don't forget about the fairies and how you're essentially imprisoning them in little glass jars against their will. In The Legend of Zelda: The Wind Waker, their expression when bottled is clearly visible, and pitifully sad.
Also in Wind Waker, the pigs can kill you. Especially on Windfall Island, where there are so many of them; if you attack one long enough, ALL of them will turn red, surround you, and literally attack and try to kill you.
Not to mention that later on in the game, there's a giant black pig on Link's home island which can do 3 hearts of damage if you tick it off. That's more than any boss, including the final boss himself.
When pillaging the various lookout towers, many times you will knock a Bokoblin off the edge. Sometimes, though, the Bokoblin will catch onto the side to prevent himself from falling. In response to this, you can actually stab his hands to make him fall to his doom. Also, the Fire Arrows will make a Bokoblin run around frantically while burning, obviously in pain. This gets even better when he runs into one or three of his comrades and accidentally sets them alight as well. Who knew you could be such a bastard in a cartoony Zelda game?
One particularly horrible/wonderful thing you can do to Bokoblins in Wind Waker occurs in an early lava-themed dungeon, in a room where a thin rope bridge covers a gap over lava. It is possible to use Link's spin attack to sever some but not all of the ropes holding the bridge up, causing the bridge to be weakened; it'll hold his weight, but not the weight of two people. After cutting the ropes, you can bait a Bokoblin onto the bridge. It snaps under the weight. The player can guide Link to safety with quick reflexes, but the Bokoblin is not so lucky, and it falls into the lava.
During the final battle with Ganon, it appears that there's no Boss Arena Recovery. Actually, you can...hookshoot your helper Zelda to steal some hearts from her...
Violence against chickens has actually become a staple of any longtime fan's playing experience, mainly because the retribution eventually inflicted upon you has become a Running Gag in the series, one that reached its logical conclusion in the The Legend of Zelda Oracle games, where if you bothered the chicken enough, a giant chicken twice the size of Link himself would show up to kill him.
And then there's in Link's Awakening, where you can eventually get Marin to cheer you on as you slaughter her chickens.
In The Legend of Zelda: Four Swords Adventures you can actually weaponise the chickens' vengeful fury in the battle mode by attacking a chicken then hiding in a house or cave while the swarm assaults any players unfortunate enough to be stuck outside.
Kakariko's cursed family in Ocarina of Time, unlike most friendly NPCs, will register sword hits. You can't actually kill them, but you can make them scream in agony repeatedly.
In The Legend of Zelda: Twilight Princess, beating chickens lets you take control of their bodies, and you can make them jump into lakes or off tall structures. If you spot a pair of boar riders aimed at a cliff — and the game helpfully spawns some every time you enter Hyrule Field — shoot the boar. It will scream in pain and sprint cleanly off the cliff, dragging its panicked riders with it.
In an uncommon example, consider the Poes, whose souls you rip out from their bodies, and they writhe in agony as they boil away.
Hit her too many times, though, and she'll crush you.
Ironically, you need to attack her a few times; it's the only way to get her to drop an item that she can't set down in a fixed location.
What is really fun is standing in the middle of some sand, then attacking her. She runs out onto the sand and then sinks.
You can also fire a cannon at birds, cow-spotted pigs, and golden dolphins. Or you can use it to kill adorable flying elephant things that try to charge you that would be scared away just by blowing the whistle.
When Ferrus is taking pictures beside the train tracks, you can hit him with a cannonball for a satisfying little yelp.
In OoT, you can throw a chicken into the ravine on the way to the Gerudo fortress. Or for added fun, you can grab it and jump into the ravine, making it flap its wings furiously trying desperately to keep itself aloft with your added weight.
After you've emptied the well in OoT, throw all seven chickens down there. Then start dropping bombs. Totally worth the inevitable chicken revenge.
In the Wind Temple of Wind Waker, there is a room with a huge bladed anvil that slides back and forth. Guess what happens when the player decides to force poor little Makar to stand in its way?
In The Legend of Zelda: Majora's Mask, you can either hit Sakon with your sword, or if you've made it through Woodfall Temple you can shoot him with your bow. Doing the latter will detonate the explosives he's carrying.
There's also a man in a tree outside the comet observatory. If you roll into the tree, you can knock him out of it, leaving him to clutch his injured leg while you take the rupees he was stealing from a crow.
Speaking of cruel rupee collection, you can also choose to sell Zora eggs to the Curiosity Shop Owner for 20 rupees each. Hope those few extra rupees are worth selling Zora infants into slavery, assuming they survive their containment long enough to hatch.
The Legend of Zelda: Skyward Sword mixes the chicken formula up a bit with Skyloft's Remlit population. The small, kitten-like creatures are completely docile in the daytime, but at night, they become highly aggressive, and the only way to make them stop attacking you is by giving them a few well-placed sword swipes. After you've done that, you can go ahead and toss the little creeps off the edge of Skyloft for extra satisfaction, but they'll save themselves by flying back up with their ears.
The real cruelty potential comes out if you give the letter to the ghost hand. Visit Cawlin soon after that, and he'll complain of constant nightmares. Visit his room that night, and witness Cawlin whimpering in terror in his sleep while the ghost hand caresses him, having fallen in love with him. That's right, you not only broke his heart, you condemned him to a lifetime of night terrors.
In the Fire Sanctuary, there are two mogmas hanging in the air. While you cannot hit them with an arrow, the slingshot, beetle, and gust bellows all hit them.
You can drop hornets' nests on top of Bokoblins, making them run around shrieking in pain and desperately trying to swat the insects away.
If you're really, really disturbed, someone made a Game Mod that lets you go outright Grand Theft Auto on Hyrule's NPCs in Ocarina of Time. As in, go up to absolutely any friendly NPC in the game (human, animal or otherwise) and kill them with any weapons Link has as his disposal. And they don't exactly just disappear when killed either... Here's an article about it.
The survival adventure game Raw Danger allows you control of several characters, each of whom get multiple opportunities to be a giant prick, from insulting people to out-and-out murder one.
In Blood Omen: Legacy of Kain, you end up traveling through several towns and villages, and are free to slice up anybody you see and suck their blood. The game has a day/night cycle, which means you can break into people's beds and kill them in their sleep. And that's not even going into the items you can use, which include shuriken which instantly flay the flesh from enemies' bones, and an orb which forms a mini black hole centralized on your target, crunching them into the size of a marble. Kain himself describes that last item as "the cruelest" of the powers he employs.
Not to mention, the game's equivalent of shops are fonts where you sacrifice some of your blood for items. Later in the game, you get the power to mind control other people, and bleeding them to death for items is a highly beneficial activity. "Nobody says it is Kain's blood that has to be sacrificed."
Using your vehicle's laser gun, you can shoot at friendly boats and airships in the bay in Beyond Good & Evil. They'll shout funny things at you (one of them is even a friend of your family, who calls you out on being a jerk) until they get really annoyed, at which point they call the cops. The cops will fine you... if you don't evade them and escape first.
You can also use your Disc Launcher to kill the green spiders in certain areas, which are otherwise completely and totally harmless. But they spit out money!
The video game adaptation of X-Men Origins: Wolverine is MADE of this trope. You're dealing with a man who has indestructible metal claws. People are going to be dismembered. Not to mention quick kills, environmental kills, and the VAST majority of ways you can literally tear people apart. It's a very satisfying game for that reason.
Ōkami. You start out being able to tackle people and bite them. By the time you reach the endgame, you can explode, shock, freeze, and burn any NPC in the game, from innocent shopkeepers to kittens.
You may also headbutt those kittens off the cat tower to have them plunge to their deaths.
Shadow of the Colossus makes it nearly impossible for you to kill your horse, but you can still shoot an exploding arrow at him (the blast will simply cause him to fall over, limp a bit, then right himself up). With excellent timing, (as the exploding arrows take longer to adjust into position and don't launch as quickly as regular arrows), you can shoot one of these suckers into the eye of the tenth colossus.
Batman: Arkham Asylum lets you have some real fun in the challenge rooms. So there are five guys patrolling with guns, meaning you need to stick to the shadows and use stealth. Excellent! Sneak up on a guy and take him down, leaving his buddies panicking! Blow up a wall, knocking down two guys at once! Grab a guy and leave him hanging from a gargoyle — then, when his buddies come to look him over, use a Batarang to cut the tether and scare the crap out of 'em! You can also spray some of your gel right next to them, then set it off when their friends come to check it out.
Batman: Arkham City brings back all of the tricks from the first game and adds a few more. Encase a goon in ice, and then leave an explosive gel trap for the poor fool who tries to free him. Use your remote stun gun to send an armored foe flying into some of his friends. Wait for a foe to set a mine, then activate the mine he just set off. Or just use a gadget to render their guns useless, drop right in front of a foe, then get the double Oh, Crap reaction of "It's Batman!" and "My gun is jammed!"
While explosive gel typically doesn't harm enemies that much, a fun trick to do is upgrade the gel to go off by proximity, leave some at the top of a ladder, and wait for the fun.
A pettier example: during the Mr. Freeze boss fight, you can smash the statues Freeze made of his wife.
Since it's a simulation within a simulation, you can have Batman run a crime scene of a virtual-reality ragdoll getting hit by a surprisingly high-speed old car. Then rewind. Then smash his legs in again. Then rewind. As long as you want. Too bad they didn't think of having Alfred say "Are you trying to release your more violent urges with trigger-buttons or do you just like seeing high-quality slapstick smurfs?".
Messiah, among other things, lets you possess someone, make them jump off a ledge so that they break their legs, then listen to their distressed screams of pain.