In We Love Katamari there's a series of levels where a sumo wrestler replaces the Katamari. Sucking people into his belly was... fantastic.
Go ahead, try to find someone who hasn't shot those poor animals a single time in Boom Blox. Its sequel even has achievements for hitting them a number of times.
Lemmings is a classic example of this: there are lots of ways for the little things to die. Most levels will have a trap of some sort, including falling off the bottom or into water, or if you fall too far and splat. Or you could always just use the nuke button: ostensibly a way of aborting the level, but quickly became popular with frustrated gamers who would gather the lemmings into a small area and make them all explode in showers of confetti, the chorus of "OH NO!" just the icing on the cake. And there was even a level where you had to only save 10 lemmings out of 80, letting the rest of them splat. It's fun! (Notably, however, there is a non-trivial 100% solution to the same level...)
LEGO Harry Potter: Years 1-4 and Years 5-7 have this in a larger volume than other LEGO games, letting you buy charms to perform silly actions on teammates and NPCs. You can later play as dark wizards, who can kill with the Cruciatus and Avada Kedavra curses, and victims don't respawn until you restart.
In Catherine, you can shove the sheep trying to climb the block tower with you to their deaths, lead them over spike blocks that cause them to explode in a spray of blood, or even squash them with heavy blocks. And remember, all of them are innocent victims of the nightmare, just like you.
You can also do this to your girlfriend Katherine if you want. You monster.
You're also allowed to inflict emotional cruelty on your fellow sheep in the game's downtime sections. Do this enough and you'll hear a news item in the waking world that so-and-so was found dead in his bed...
Warp has plenty of potential body horror allowed by its teleportation mechanics. Possess a human and detonate them from the inside, trick a guard or turret into firing on humans by drawing their fire with a echo-decoy, traumatize a scientist for life by possessing him and then switching locations with another human, thus teleporting him into another human and detonating the latter in a shower of gore...
Portal has the turrets that have an innocent voice but are quite quick to shoot you full of holes. You can only disable a turret by knocking it over, but there's plenty of ways to do so. Drop a cube on their heads, smack them around with another turret, or even disintegrate them and hear them scream "ow" several times.
At one point you are required to tamper with the turret assembly line, causing freshly built turrets to be thrown into an incinerator. Its a case of But Thou Must!, sure, but there's nothing stopping you from standing on the walkway as long as you want, listening to them scream as they're tossed in one-by-one.
There is nothing that will prevent you from actively killing your teammate in the coop mode, at certain points GLaDOS will try to convince the players to betray each other or that their partner is doing this do them. There are even arbitrary "science collaboration points" handed out for various reasons to try to make it a competition. Lampshaded by many of GLaDOS's and Cave Johnson's quotes, which state that humans cannot collaborate and will betray each other.
Crush your partner once with moving blocks and GLaDOS will give you points for teaching a lesson in trust, do it a second time and she takes it away as you had already taught the lesson. Do it a third time, and she gives you bonus points for being blatantly cruel.
Pushing a stretcher loaded with a wounded survivor under a ceiling that's too low, so that the survivor is knocked off the stretcher.
Activating a conveyor belt with a child on it so that the child falls off the end, hits the floor below, screams "ow", and rolls over clutching a broken leg.
Scribblenauts is ripe for opportunities to be needlessly cruel. Quest-wise, there are many situations that can be solved with perfectly sensible means, but that you can solve just as well with a flamethrower or a minigun; however, the game's open nature also allows you to be cruel just for the hell of it.
A boy wants to go to school, but there's a bully called Duce blocking his way, and he asks you to help. You can add the "friendly" adjective to Duce so he'll let the boy pass... or you can give the boy a baseball bat.
Want to spawn a dozen babies, toss them in a hole, and then drop anvils on them? Sure, why not?
Even the normally straight-faced ESRB got in on the act: part of the game's infamous rating description includes the beautiful phrase "steak can be attached to a baby to attract lions".
In Bugs Bunny & Taz: Time Busters, you are perfectly free to kill the other player/character. Taz can bite, spin, or toss Bugs off a cliff. Bugs can kick, snipe, or throw bombs at Taz. And if you're playing solo, you can make the other character do absolutely anything for a laugh: whether that be standing in position to get crushed by Gruesome Gorilla, distract some mooks, or jump into lava!