It's possible to get Rebecca killed, but it involves ignoring her for over 10 minutes, much longer than most players will. A much easier way is to exit the room once you find her without killing the Hunter, which will immediately kill her the moment you leave.
In the REmake, you can refuse to give Barry his revolver back, which gets him killed by Lisa. However, it is highly recommended to do so in a speed run as you will not have to fight the final boss (saving a few minutes), and his magnum is the second-most powerful weapon in the game capable of killing almost anything with one shot, including the Tyrant (again, saving a minute or two).
The HD version has Achievements/Trophies for finishing the game with both NPC companions, one of them, and neither of them. Do you want to be a hero, or do you want to get all of the Achievements?
Fatal Frame II gives you Mayu Amakura, the protagonist's twinsister. While she's supposed to invoke the opposite reaction, she can be pushed around when she's in the way and her inactive role around violent spirits makes her excellent bait for Zero Shots. Have her get attacked repeatedly or for those extra few seconds, until the camera gives you the signal for a Zero Shot.
ObsCure: The Aftermath will let you bludgeon your partner as much as you want, with baseball bats, hockey sticks, and more. All you get for it is a spray of blood and an indignant response, though, it doesn't actually hurt them... but that's a good thing when the two of you are fighting the undead in close quarters. (And oddly enough, projectile weapons don't have any effect on your partner.)
Haunting Ground: The alchemy room allows Fiona to forge items for herself and Hewie. Most are helpful (reduce Panic/raise Stamina) - but some do the opposite (one of Hewie's items actually causes him to become aggressive towards Fiona - even at the highest possible relationship level). Using such items or attacking Hewie directly is actually necessary to get the bad ending (and no, just ignoring him isn't sufficient; his relationship value has to be low enough for him to attack Fiona to get the ending).
Also, there are various death traps throughout the game such as an Iron Maiden, which works as great a hiding place as one would expect; most are glaringly obvious and there just to see Fiona die in a creative way/unlock cutscenes in the Bonus Room.
Hell Night doesn't seem like a game that could have the potential, but since your partners die as soon as you're caught by the monster, that's been chasing the player constantly, it's possible just to get hit on purpose. If you can spend time enough and even survive long enough to return to the Mesh (a safe hub-level), you can kill off all the partners in the game. You get a bad ending, too.
Plenty of this in the STALKER series. Oh look, a wounded guy on the ground. He needs a medkit. Do you heal him and give up valuable equipment, or finish him off (or let the local wildlife kill him) to loot his corpse? Or heal him, trade with him, then shoot him and loot him? Or even better, heal him, trade with him, then let him be torn to shreds by that pack of wild dogs over there and then loot his corpse? Hey, there's a guy who just helped you out. Do you thank him and leave him be, or shoot him in the face now that he's of no further use so you can get the unique weapon he's carrying? Do you warn those Loners that a group of Bandits are going to try to kill them, or side with the bandits themselves?
If you play your cards right in the "End of the Road" scenario in Resident Evil: Outbreak File #2, you'll be followed around by Linda, an NPC scientist who moves slowly due to a gunshot wound to the leg. If she's struck by enemy attack, she's simply knocked over and does not appear to take damage. This makes it possible to run ahead of her and use her to clear minefields for you.
Silent Hill 2. The various endings depend on how well you treat your companion. Listen to her advice, her thoughts, her emotions is good. Ignoring her, running off, treating her like a moron...well, things happennote Although the latter result may possibly lead to a happier ending for the protagonist, once this companion's true purpose is understood..