In Kingdom of Loathing, certain objects are defined as alive in their descriptions; destroying said objects seems especially cruel. Two ways of destroying objects are smashing personal equipment, and having a Comma Chameleon eat familiar equipment. "Living" equipment includes: A (talking) miniature dormouse; Rhesus Monkey; Turtles (who are used as helmets)...
Hell, Turtle Taming in general. This is the item description for the Torquoise ring: "You convinced this torquise to grab and hold onto a ring setting, probably by threatening it with your pliers."
The Wings of the Goddess expansion of Final Fantasy XI introduced two monsters that are mostly harmless and/or beneficial: Lycopodiums and Pixies. Lycopodiums are a non-aggressive variant of the Mandragora (which is about the size and stature of a toddler) that follow players around and dance, providing the player with Regen if s/he has completed a quest. Pixies will heal and resurrect dead players whenever in range. In spite of this, players are not above carting groups of innocent, dancing Lycopodiums to their doom or killing pixies on sight. To make matters worse, pixies are known to drop Stygian Ash, a necessary item for claiming the notorious monster, Dark Ixion, giving players further justification for killing them.
And people wonder why Lycopodiums and Pixies went extinct.
In the classic BBS game Tradewars 2002, you could create a planet and then fly to Earth, land your spaceship, load up the cargo holds with millions of colonists eager to go into space, and bring them to your new world. Or, if you wanted to become evil so you could rob and steal and such, you could load up your cargo holds with millions of colonists, and then eject all of them into empty space; the game "rewarded" you for this by lowering your alignment.
This exact same trick is also usable in Starport Galactic Empires, for the same reason. You could also eject people who have hired you to fly them to a different port.
In RuneScape, baby trolls will eat all tradable items, as well as a few untradable ones. Pets are one of the things you can feed to your troll.
Trolls are named after the first thing that they eat. Sometimes, the item name does not become the Baby Troll's name. For example, "Troll Lieutenant's Bones" becomes "My Own Dad."
In Dofus, in order to practice the enhancement and modification of magic items, one must use lots and lots of magic runes on items to practice. The runes come from getting items which enhance stats, and smashing them to extract the magic runes. Through a variety of ways, one can come into possession of "Bow Meows," which are cute and cuddly little kitties which follow you around. If you feed these kitties twice a day, they develop abilities to boost your stats... and since they are easy to get, they are a popular rune source. Alternately, there are some crafting recipes and the like which require one to skin a Bow Meow and use their ghost as an ingredient..
In World of Warcraft, there is a quest in Hillsbrad Foothills called "Do the Right Thing." You are given the quest after you see that there are humans buried in the ground with their heads sticking out, with Scourge roaming around in the area. Since you cannot allow the Scourge to reinforce their numbers by using the humans something has to be done about it. You are given the option of pulling the human out and letting him go free, but you are also given the option of bashing the humans heads in with a shovel you were given upon accepting the quest. Even more hilarious is that their heads EXPLODE upon doing this. Killing them even comes with its own debuff.
One quest in Tirisfal Glades has you feed a pumpkin to a captured Scarlet Crusade member right outside where you get the quest. The pumpkin is laced with a potion that turns him into a ghoul, and then he breaks in half a few seconds later as if though he's been slain and of course respawns. Shame you can only do it once.
The Death Knight's Corpse Explosion spell can be used to blow up corpses of dead mobs and players for when mocking them by using an emote just won't cut it.
In the Valley of the Four Winds you'll sometimes find a large baby crocolisk named Manglemaw eating at the bodies of dead cranes. Kill it, then you'll invoke the wrath of its mother which has grown in size from the properties of the water, then you can kill her and loot her tail to turn in for a few gold. It's already established that your character is not above child murder given the dragon whelps and similar newborn creatures that you've probably killed, but still.
If you're tired of virmen taking up residence in your soil patches in Sunsong Ranch after you harvest a crop, then you can simply run over the little bastards with the plow you can get when you reach Exalted with the Tillers, which will actually stun them and take off 70% of their health. (Though some may prefer to do this because it's pragmatic, not because it's cruel.)
Speaking of virmen, one quest has you throwing turnips painted orange at them. They hop over to them, thinking it's a weird carrot of some kind, and run away in fear and confusion when it's revealed to be a turnip. You can keep throwing orange turnips at these virmen as long as you have the quest. (Eventually, to progress in this zone, you do need to turn the quest in, and the quest item doesn't work outside that area.)
In the Siege of Orgrimmar raid, the first thing you see once you make it through the main gate into the city is Ji Firepaw about to be executed by Kor'kron forces when a nearby candle goes out. What's supposed to happen is that you kill the overseer about to kill him and Aysa Cloudsinger carries him out; the overseer will kill Ji if you wait too long, and upon seeing him die Aysa will attempt a Roaring Rampage of Revenge with predictable results. So in the end, you've let the pandaren's ambassadors to both the Alliance and Horde die pointlessly. You Bastard.
In one area of Frostfire Ridge, there are two Thunderlord orcs trying to restrain an ogron. Attacking them or the ogron will cause the ogron to launch them upward and forward and they'll die upon hitting the floor.
There's a couple of enemies in Spiral Knights that are rare spawns. Two of them - the Love Puppy and Mewkat - are harmless (and the Love Puppy will even heal you). However, they can drop rare items... Or they might spawn in an arena where all enemies must be killed to move on...
There is no shortage of awful things you can do in WildStar. Blow up poachers with mind-controlled rhinos? Sure. Assist the Chua with their experiments, almost all of which involve killing, maiming, or exploding something? Why not. Kill some innocent sheep or scare them into mines to watch them blow up? We're ashamed you thought you couldn't do that in the first place.
In Star Wars: The Old Republic, the Force-Lightning-centered Sith Inquisitor infamously has the option to electrocute people in conversations. That's not this trope—it's Played for Laughs most of the time, and the rest of the time you need information or have another good reason to do so. What is this trope is choosing to shock your own teammates.
The Bounty Hunter can be horrifically verbally abusive to Blizz, who is pretty much the living embodiment of cuteness, energy, and happiness.
Sith Warriors can not only keep Vette's Shock Collar on, but activate it every time she so much as opens her mouth. Then they can give the control to Jaesa, who quite possibly spams it more than they do.
The Sith Pureblood social ability is "Punish," which delivers a backhand slap to their companion, making them cry.