In La Pucelle you are encouraged to take the monsters that you purified, put into your party, and loved and nurtured to trust you...and sell them into eternal slavery to the Dark World. You are encouraged to do this as the Dark World will send you gifts for any accomplishments that monster does, such as working through the ranks to Demon Lord or Overlord. In addition, the process fuses any items they had together. Maybe there's a reason Prier is a Demon Overlord in the Disgaea games...
Granted, that "loving and nurturing" you did involved stuff ranging from making them break blocks and do push ups to turning them into cyborgs and even shooting them (Granted, you have to build up their trust a number of times before they wouldn't quit over that last one).
If Montblanc is killed mid-game, his storyline scenes are replaced with the arguably much more interesting character Ezel Berbier. Some players actually kill Montblanc just to replace the annoying storyline companion with the more interesting one.
In Final Fantasy Tactics pretty much from the very beginning, you can pass over Mandalia Plains repeatedly until you get a random encounter. The enemies' party will invariably have a yellow chocobo in it and you can kill off everyone else in its party, then surround it and attack it virtually endlessly as its only healing action, Choco Cure, also heals characters on all four sides, thus giving you a way to level up and get a hell of a lot of jp to boot, and joy of all joys, all you have to do is torture a sad-faced chocobo forever.
It doesn't stop there. You can attack your fellow party members for experience and/or job points, invite people into your party just to take their gear and kick them out, or murder your own teammates, wait for their Final Death and eat their soul absorb their crystal to instantly learn the skills they did. You can also raise monsters only to kill them permanently for their "skins" (which can them be traded for rare items in certain shops).
Tear gas and stun grenades let you do the same thing. You can also, in the 1.13 mod, throw molotov cocktails onto unconscious/stunned enemies.
It is a common occurrence in Fire Emblem games for there to be a non-recruitable friend/mentor figure/family member/lover/etc. of one of the player's characters on the enemy side. If one so chooses, he can make them the one to do their loved ones in. Usually, they get a special battle conversation for that.
And then there's the common occurrence of having said friend/mentor figure/family member/lover/etc. being on the same team as said player's characters. With the game's concept of Final Death and even having a few plotline deaths, you can pretty much ruin someone's day by killing off their partner.
Star Trek: Birth Of The Federation can implement this trope. Though you're usually given a diplomatic option (an option you're encouraged to use if you play as the Federation), you can simply choose to subjugate or destroy other races. In fact, your people will actually be happier with you for choosing these options if you're playing as the Cardassians (in the case of the former) or the Klingons (in the case of the latter).
In the otherwise excellent old game No Greater Glory, a simulation of the US Civil War, your score if you won depended on how well you had brought your country through the war, and evaluated you on the basis of four criteria: popular support, finance, diplomacy, and peace terms. You will note what is missing from that list: casualties. The number of men you had killed on either side over the course of the war has no effect on your final score, so if sacrificing more of your own men would improve your performance in one of the four categories, the game would register that as a better and higher-scoring performance. What that often meant in practice was that if you knew you were about to win, you could juice your score by grabbing areas that you didn't need to win, even if that meant both inflicting and taking unnecessary casualties.
A favorite late-game battlescape tactic in X-COM 1 and 2 is to mind-control the first enemy you see and use him as a very expendable scout to locate his nearest friends. Mind control them as well and repeat until the entire alien force is under your control. Then herd them all into a nice big group, and force them to drop a couple HE or stun grenades at their own feet. Sometimes it's so effective you can wrap up a ground assault or terror mission on one turn without any of your own troops so much as leaving the ship. And even if a few baddies escaped your notice, they're likely to be so terrified and demoralized that they'll throw down their weapons and run about aimlessly.
The reboot offers its own method, overlapping with Combat Pragmatist. There's a room ahead, and you can't see what's in it, but there doesn't seem to be much cover. Eh, send the New Meat in to Leeroy Jenkins his way in and get a line of sight into the room, with one of your precious high-leveled Heavy troopers near the door to lob a rocket in if there's a group of aliens clustered together.
Mutons, with their low Will, make for very expedient suicide bombers. Just mind-control one and have him charge into a room with enemies, get next to the enemy you most want dead, and have him chuck a grenade at his feet.
Super Robot Wars UX: In the chapter where Jin deploys with his first ever squad he leads. When you shoot them down, he casts Spirit Commands in anger and sorrow; Spirit, Strike, and Valor. When the last subordinate is shot down, a sad music begins to play. You can leave them alone so this doesn't happen, but they die anyways when the Island detonates with the Fenrir.
Some of the most interesting dialogue in Pokémon Conquest is the character's response to being teamkilled.
Eador has random events with moral choices, so if traders are looking to buy some virgins, the player can refuse, accept, or have the traders killed and take their gold. Among the more creative options, the player can have shipwreck survivors killed and loot their wreck, force subjects to farm poisonous spiders and sell the silk, hire adventurers to clear out a dungeon and have them killed for the loot, kill babies, eat a mermaid, or eat a unicorn and have the chef executed when it tastes disgusting. The ever-popular favorite: a band of hunters can bring in captive evil sorcerers. The player can have the hunters flogged to get an item from the sorcerers, then have the sorcerers tortured to make them spill their magic. The good and neutral choices are not deranged, and it's a bit weird how good-aligned players can go along holding festivals and rewarding adventurers like normal people, while evil-aligned ones descend into madness.
The game Stalin's Dilemma, by Edward Bever, as you might guess from the title, abounds in this. The question is not whether you will kill millions of people, but how many millions. If you keep the death toll below ten million while improving your industrial output and military capabilities to the point where you can win World War II, while simultaneously maintaining political stability, you are rated as a hero of the human race. If you want, though, you can go full Stalin and just see how many millions of people you can kill.