Battlefront 2: the award for getting four critical hits on a vehicle with a rocket launcher in one life is a remote-guided cruise missile launcher. Which you can use to snipe enemy infantry. Without giving them the remotest hint of a chance at shooting back. MUAHAHAHAHA!
In the Oddworld series, you can kill and/or beat the creatures you're supposed to save or the ones you possess in a myriad of ways. But probably the cruelest of them is presented in Oddworld: Abe's Exoddus. Follow the steps:
Step 1: Find a depressive Mudokon
Step 2: Slap him
Step 3: Watch him kill himself by tapping his forehead
Line up ten Mudokons in a row. Slap the Mudokon on the left of the line. Escape to the right of the line of Mudokons. The first Mudokon will get angry and swing his arm in your direction... hitting another Mudokon, who gets angry, and slaps the first Mudokon back, as well as the other Mudokon standing on the other side of him. This continues until everyone's hitting each other. Suddenly, one of the Mudokons falls down dead. Cue all the depressed Mudokons slapping themselves in the head until they die.
Ask many Mudokons to follow you. Tell them to wait. Walk behind an electric barrier that has been turned off. Turn it on. Tell the Mudokons to follow. Enjoy several cries of "Aaaaaaahhhh!!!" before Abe says "Whoops..."
Ask a blind Mudokon to follow you. He will continue walking in that direction until you tell him to stop. Enjoy watching him bounce painfully off of walls a few times before leading him to a meat grinder.
This isn't even mentioning pulling the various levers in the first level without getting the hapless Mudokon cleaner to move first.
Possess a Slig, then after using it to do whatever has to be done, stand with its back to a drop and just hold down the fire control until recoil pushes it over the edge. It'll be dead, and you'll be glad.
There's actually a special ending if you kill as many Mudokons as possible (apart from the ones you have to save).
In Star Wars: The Force Unleashed you can break almost anything. Including the windows of space ships that will pull out everything and everyone near them before the hole is automatically sealed.
First, find a battle with human opponents. Kill everyone except one person, then grab that person with the Force and lift them into the air. You can bounce them off walls and the ceiling and make them do flips in midair, all while they scream for help.
Out of all the things you can do in the game, the absolute cruelest thing happens in the last level of the game. You're on the Death Star, which is putting the weapon through its test runs. This means that throughout much of the level, you'll be ducking out of the way a planet-destroying laser as you crawl through its inner systems. Those poor stormtroopers.. all you gotta do is let the weapon fire off, Force Hold them in the air and wait...
In Total Overdose: A Gunslinger's Tale in Mexico, another driver/shooter, between missions during sandbox wandering, the player can pretty much commit any violence to civilians without consequence. When hijacking, the driver is pushed to the passenger's seat and remains in the vehicle, and will make panicked comments in Spanish when the player leaps from it while in motion. Since all vehicles are Made of Explodium, even if it coasts to a halt to lightly tap an obstacle, it and the driver will immediately turn into a spectacular ball of flame.
Also in sandbox mode, floating red skulls can be found which initiate the 'Day of the Dead' minigame, in which random hordes of Day of the Dead revelers dressed in skeleton costumes appear and assault the player with a subset of weapons (a good way to stock up on ammo). When the game times out, the celebrants fade back into normal civilians, dying from whatever weapon crosshair was on them at the time.
Also in sandbox mode, the player can find chaingun turrets at random and implausible locations. Using one is the only time police will rally, and the gun's only purpose is to blast as many of them as possible for the largest kill streak. The weapon's power easily explodes police cars within a second of sustained fire, killing police inside and around the vehicle, and often triggering a chain reaction that guarantees collateral damage among civilians as well.
Mercenaries: Playground of Destruction lends itself to this. Especially when you unlock the aptly-named Cheat Crate and discover within...the portable air strike. Ever wanted to level significant chunks of North Korea? Or indeed any concentration of life and architecture?
"Don't take my car, don't take my - nevermind."
In BloodRayne, in the mines, you may notice a few doors have been barricaded from the inside with a few Nazis hiding in them. Rayne will actively taunt these poor fellows who are just hiding from the Daemites, even though they offer no resistance, in fact they are out right cowering. They are free health should you need it, but damn.
BloodRayne 2 meanwhile, has many, many different ways you can dismember the human body.
Psi-Ops: The Mindgate Conspiracy is basically designed to be able to mine as much out of this trope as possible. An extremely understated list of what you can do to enemies in the game includes: Shooting them with a few different normal guns, using telekinesis to throw them off precipices, through windows, into walls, into each other, into electrified fences or equipment, using mind control to cause them to shoot each other, themselves, walk into the path of a particle accelerator or off a roof, psionically draining their brains until their heads violently explode, and you know, fire.
In fact, the game's mechanics practically encourage cruelty: weapons are relatively weak, and ammo scarce; psi powers drain your meter quickly, with the exception of mind drain. Solution? Use a combination of telekinesis and Mind Drain to yank a foe towards you; drain him of his "psychic energy," causing him to flail around in the air, gibbering incoherently until his head pops like a watermelon with a lit firecracker stuffed in; shampoo rinse repeat. This works on all mooks save the ones in anti-psychic armor, and is a great way to top off the old mind-woogie-juice in mid-fight.
Being based on much the same premise, Second Sight lets you perform similar acts of cruelty. It's possible to not only choke your enemies to death with telekinesis, but then to use their bodies as missiles against those enemies still living, if they haven't run away screaming in terror, that is. You can grab an enemy from behind and drag him for use as a meat shield, his comrades won't shoot but you can... So they may get fed up and shoot your hostage anyway.
The protagonist of the Wild West video game GUN has, amongst his arsenal, dynamite arrows. This is exactly as awesome as it sounds. The "cruelty" part comes in when you use it on civilians - they react to being hurt first and start running away, only to explode three seconds later. This works especially well since civilians react appropriately to thrown dynamite, but treat dynamite arrows just like normal arrows. For more fun, shoot hookers; rather than running away, they'll run towards you with the intent of knifing you. Just make sure you do it a safe distance away.
Gun also allowed you to scalp people after nearly killing them with gruesome results.
The 2005 The Punisher game allowed you to brutally interrogate people for information and/or your sick enjoyment. The four standard methods included choking, punching, threatening with a pistol, or smashing their face against the ground. Specialty interrogations included feeding them into a wood chipper or a crematorium and this troper's favourite, threatening them with getting gored by a rhinoceros. If you killed them after spilling the beans, you lost points. There were also specialty executions involving shoving them face first into a bear trap and shoving the barrel of a flame thrower into their mouth and pulling the trigger. That said, sparing them inside the deathtraps is as cruel as finishing them off.
Tethering deserves a line of its own. Tether someone on a vehicle going across a bridge, and there's a good chance they'll go over the side, being suspended in the air all the way to the end of the bridge - and then smacked into concrete. Tether someone to a gas canister, then shoot the canister and watch as it flies into the distance, dragging the enemy along with it until it blows up. Tether someone to a fuel barrel, shoot it and it'll rocket straight up, carrying the person along for the ride. Then it blows up, letting the poor sap plummet to the ground. Get a plane, fly it alongside another plane, jump out of the cockpit and on your plane, tether the two planes together and cause the civilian plane to lose control by pulling it around... or just jump off and see how much of an adverse effect an inert military jet has on an airliner's flight plan.
Let us just say that Crusader: No Remorse and its follow-up No Regret are aptly-titled when it comes to what you can do to people.
In Syphon Filter you are rewarded for killing Mooks in certain conditions and styles. By using stealth kills, killing them with darts, knives or headshots. Doing so will unlock new weapons and you can carry more darts.
Jet Force Gemini. You can pick up the heads of both fallen enemies and the teddy bear things you're supposed to be saving (this counts as "saving" them, incidentally). Two late-game weapons are short-range, low-damage guns that exist solely to allow you to slowly and painfully kill your enemies (either by setting them on fire or electrocution). You can slaughter enemies after they've surrendered (actually a good idea, since they like to pull grenades on you when you turn your back).
In Slave Zero, you take on the role of a giant 60 story tall robot. Among the actions you can take are stepping on pedestrians and cars, or you can pick them up and use them as increased mass for your punches - or throw them at your enemies, though the damage is minimal. Ah, but see that civilian structure that surely houses many innocent families? Destroy it and you'll almost invariably find ammunition, health or items such as girders that can be used as clubs. The main character is working to save the city, but you wouldn't think it from the destruction he leaves in his path...
Max Payne titles generally let you have fun with the corpse physics. They are usually good on making noncombatants run or hide, but quick and cruel trigger fingers can nail some civvies for Max's body count.
The Grand Theft Auto series is full of examples of this trope, with numerous weapons, including baseball bats, knives, guns, RPG launchers, Molotov Cocktails, grenades, and cars that can be used on enemies, police officers, allies, and innocent civilians. Not to mention, in Grand Theft Auto IV, there are various places (such as Rotterdam Hill) where one can push people to their death, or just push them down the stairs.