Age of Empires and games derived from it make killing civilians a sound tactical move. Then again, most of the games are set before the Geneva Conventions and most civilians can take up weapons and attack the enemy anyway...
Age of Empires III added a physics engine, which is best put to use by training a force of 5 Falconet cannons, sending them to attack a single enemy villager, and watching him scream and fly about 7 feet straight up in the air before landing headfirst on the ground.
The local source of resources is Green Rocks that horribly mutate anyone who stands in it unprotected. It's perfectly possible to simply fill the streets with the stuff, making it impossible for the civilians to get out without dying, all to increase your profit margin.
In the first person shooter Command & Conquer: Renegade, you are actually encouraged by the tutorial to squish people while in a Medium Tank. As in they actually set up helpless Nod soldiers for you to run over as part of the tutorial. Hotwire even has a sadistic tone in her voice as she tells you that you can squish infantry.
Feeling bored? Try marching your troops across a Tiberium field for shits and giggles - they'll die and mutate into creatures of living goo called Visceroids. While fun in and of itself, this turns into a surprisingly viable tactic if there's an enemy base nearby: visceroids in multiple numbers will eventually merge into extremely vicious and tough Large Visceroids. You can't control them, but they tend to attack anything close to them - like the aforementioned base - and do a ton of damage. Given that it only takes two dead infantrymen to spawn a Large Visceroid, and that the latter is frightfully more effective at destroying the enemy than the units that created it, there is plenty of motivation for doing this with enthusiasm.
While hilariously impractical, you can create a "Visceroid Farm" by building a wall around a tiberium field and air-dropping troops into it. When you're ready to release your horrors, just sell off a portion of the wall and watch them run amok. If you blow out all of the bridges to your base (a few maps do have each side isolated like this), winning the match is simply a matter of time. None of this is remotely practical, as the troops needed to produce the visceroids and needed to keep the bridges destroyed (not to mention the time) would probably have steamrolled any conceivable enemy in less time and effort.
Two GLA missions are explicitly based around the concept of "Wreck havok on innocent civilians", one of which involves hijacking relief supplies then blowing up villages for resources.
Another mission has the GLA using Toxin Tractors to slaughter civilians, with a quota of 300 civilians. For obvious reasons, this mission was cut, though was officially released for download by EA.
Many maps in the games feature large urban areas with buildings your troops can garrison. You can also choose to reduce the city to a ruined wasteland with your weapons. This is actually a rather viable tactic, as it prevents the enemy from garrisonning those buildings. Some of these buildings will even "drop" a Money / Powerup Crate when destroyed, giving you more incentive to wreck them.
Command & Conquer: Red Alert: The Playstation version has a cheat that turns the ore into civilians. They just stand there as the harvester scoops them up, and you hear their dying screams.
Yuri's faction has a structure called the Grinder, which reprocesses units for their materials. You're meant to do this with captured enemy troops, but you can also mind control innocent civilians and send them to what sounds like a horrible and grisly death. This is actually a good way to get some cash.
You can up the ante with the Genetic Mutator and some Slave Harvesters. Slave Harvesters automatically generate new slaves if the old ones die (for free) but Slaves are usually uncontrollable and are worthless in value (you can free slaves of other Yuris and they come under your control, but they're still worth a pittance if you send them into the grinder). With the Genetic Mutator, you can turn a huge cluster of slaves into Brutes, who can then be sent into the grinder for a massive cash boost. Since both the Mutator and the Slave Harvester require no money to function, doing this will get you a massive influx of cash every few minutes, making it cruel and practical. Mustache twirling optional.
Yuri's entire army seems to be based on this and trolling. Against AI enemies, you can use flying Discs to shut down the enemy bases' power and cash, but the AI won't give up unless you destroy all of it's production buildings. Refuse to do so and you can watch the AI fruitlessly try to kill you with what little cash they have left. Again, mustache twirling optional.
The Iraqi Desolator can deploy to irradiate a massive area. Any infantry (except Desolators) caught in the area will quickly die from radiation poisoning. And the same goes for any civilians...
Subverted in Tiberium Wars, in which civilians are only there for show, and then Red Alert 3 onward, where they are completely absent. Their buildings, though...
In Company of Heroes, not only can you run over infantry with tanks, but Sherman tanks can be upgraded with mine flails, a collection of weights attached via chains to a spinning motor. Their primary purpose is to destroy mines, but there's no reason why you can't use it on infantry.
The Allied forces have access to demolition charges, while the Wehrmacht can build bunkers, including medic bunkers, where their troops can huddle for safety. There's nothing preventing you from blowing up a first aid station with garrisoned troops.
Crusader Kings has this in spades, even discounting the things you'll be doingbecause it will help your dynasty, though some of it is governed by Random Events. You can assassinate little children to inherit titles, kill your wife for a new one if she doesn't provide you a proper heir, burn churches, revoke titles from your vassals for no reason at all, ruthlessly pillage enemy lands with your troops, force heathens to convert at swordpoint, and even steal relics.
Playing the Byzantine empire or Byzantine culture group? Have any captives? Castration and blinding are options available. If you castrate a child, you even get a special message.
Generally, when you do nasty stuff to your captives, they are automatically released from the dungeon... but there is an option in game rules that disables this, meaning that you can torture your prisoner endlessly....
Some mods make it even worse.
The Game of Thrones mod allows one to play as Joffrey. After crushing the Stark rebellion, the player is free to imprison the surviving Stark family members and blind/castrate/execute them.
The Reapers Due added the ability to torture, humiliate and mutilate your prisoners. Doing so will cost you piety and give you the cruel trait, so there is no real reason to do so, exept to enjoy your enemies suffering.
If you check the game's subreddit or forum, you'll see the truly insane depths that this can sink to. In fact, there's an entire video series called "Things Crusader Kings Say" based on the subreddits.
Even since Dune II, RTS players have been running over infantry in tanks. The crunching sounds just encourage you.
In a later game, Emperor: Battle for Dune, the Harkonnen light vehicle is the Buzzsaw. Unsurprisingly, it is good at destroying spice fields and infantry.
Way back in 1986, you could do this in the Origin Systems adaptation of the boardgame called Ogre; overrunning infantry with an AI-driven mega tank was not just fun but standard, orthodox tactics.
Dungeon Keeper 2 gives the player access to prisons, torture chambers, traps, fight pits, a temple where you can sacrifice your minions, and rigged casinos. So many possibilities...
Capture a group of heroes and convert all but one of them. Feed your converts, heal them, and train them while giving the odd one out only the barest amount of food and healing to survive the prison. Then drop the unconverted one into a pit and put his former friends on the sidelines to cheer as he's beaten to a pulp over and over.
Capture a hero. Drop him in the torture chamber and keep him barely alive until he gives some information. Reward him by dropping him in the fight pit with your meanest monster before returning him to prison and letting him starve to death, becoming a skeleton.
Line the walls of your hero lair with torture devices, so the heroes that serve you live surrounded by screams as you torture their former allies.
Take the monsters you don't want and lock them a sealed room without food, money, or beds. Wait until they get angry and revolt and burn them down with lightning. Have your imps send them to prison and let them rot into skeletons or vampire fodder. Or simply beat them into unconsciousness or death.
When Payday comes around, grab every minion in your domain and drop them in the Casino. Switch it to rigged and let the money roll in. Once you've got back some and the monsters begin to show displeasure, switch it back to normal and put the monsters back to work.
A monster displeases you? Stick it somewhere surrounded by lava so it can't reach the exit portal and wait for it to turn on you. Send your creatures to beat it up, then torture it into serving you. Repeat.
In Empire at War, if the Rebellion captures Coruscant and the player is the Empire, the player can use the Death Star to blow up Coruscant, killing the planet's population of over a trillion.
The various methods you finally deal with the Super Agents themselves count:
The P.A.T.R.I.O.T Agent, Ramboexpy Dirk Masters: you dunk him into a tank of chemicals that have been engineered to react violently with the steroids in his body, transforming him into a Freak. Not only is he stripped of his humanity, but he has to serve your every whim, and there is nothing he can do about it.
The A.N.V.I.L Super Agent Jet Chan: you drug his food with sedatives, and then arrange a "fair" sparring match with a minion. In the resulting match, he is so utterly and humiliatingly beaten that he retires from the agency and flees civilized society with his name and reputation in tatters, and spends the rest of his life in seclusion, meditating bitterly over his defeat.
The S.M.A.S.H Super Agent Mariana Mamba: giving her reverse-liposuction treatment and making her hideously obese. Without her primary asset - her splendid looks - she is forced to retire as an agent.
The way you deal with the H.A.M.M.E.R agent Katarina Frostanova, arguably the most cruel of all of them: you take her childhood teddy bear, the only thing she has ever shown affection for, and you order a minion to beat it up, chop it, and tear it into pieces. Right in front of her. Her resulting mental breakdown is so catastrophic that it renders her completely unfit for active duty.You Bastard!.
In Kingdom Rush: Vengeance, you play as Vez'nan's dark forces. One of the levels takes place in Linrea's farmlands, where innocent farmers will attempt to stop you — and they're all easily killed and dispatched. With the right towers or heroes you can do more horrible things to them such as turning them into zombies. You also can click on the sheep in the background to make them explode into Ludicrous Gibs, although doing so to all the sheep will cause their farmer to attack — and this particular farmer is a miniboss-level enemy that can catch you unprepared.
MechCommander allows your mechs to target and destroy civilian objects such as houses and cars (although you get no bonus for doing so—apparently civilian casualties are of no importance in the 31st century), and has the "lordbunny" cheat, which allows for infinite artillery strikes. While this has the obvious potential use of decimating enemy forces, it also can be used to annihilate huge numbers of civilian targets without wasting your mechs' ammo. You can call in dozens of artillery strikes to raze entire cities to the ground and, once all civilian buildings have been flattened, set the forests on fire, probably condemning Bambi to certain doom in the process.
In every Pikmin game, you can have control over put to 100 cute little vegetable minions whom you can do anything you want with, including throw all of them over cliffsides, feed them to bigger creatures, and this troper's personal favorite, taking every non-blue Pikmin and drowning them in a nearby body of water.
Planet Blupi: You can force the Blupis to perform many tasks without rewarding them with food, thus starving them and killing them once their energy runs out. You can also kill off Blupis by killing them in an explosion or exposing them to killer enemies.
In a mission in Sacrifice, you have to destroy a tree for one Pyro, but if you kill all the peasants around the tree, Charnel rewards you for it. Additionally you could target your own minions with spells or other minions, this is great for freeing up some souls from obsolete units.
Starcraft II has mods for custom multiplayer matches, and one of them is a mod that allows the player to spawn nearly every unit from the campaign and multiplayer (co-op not included), and edit their stats, allowing one to create a marine that uses the Kelmorian Mining Drill laser at 4x speed for 1000 damage per hit while healing 10000 Heath and having a 10000 Shield and having an armor rating of 1000 with a movement speed of nearly 160 with Kerrigan's WoL trait of not dying even when reduced to 1 health, effectively killing anything you have with range and outrunning anything that attacks you before staring at it hard enough to self-destruct. Basically, one can do a 1v7 match against 7 elite or cheating AI opponents, and create a unit that will kill everything and a base that has an ability coded not to die, effectively making you entirely invincible. From here, you just kill waves of enemies, spawn enemies to fight them, or just highlight structures and destroy them. It's just you using your omnipotent powers to crush the AI because the AI can't use the spawn-units command or edit their units. Heck, you can grant yourself one-sided vision with the enemy and control their own units as they kill their own army with no way to stop you.
The aforementioned Thor can be spawned on your side and edited. Nothing quite like a giant death machine with infinite energy and ridiculous attack speed and damage to just destroy enemy units. Because the AI is coded to back off from encounters that are too difficult, it's likely they're just going to repeatedly retreat from the Odin until you're at their front door and they don't have any choice but to defend themselves, while the AI doesn't help its own teammates because of the same AI exploit.
In Star Trek: Armada, it is possible to send members of your crew to an enemy ship to kill the crew and take over the ship. It is also possible to control a ship if you have at least one crewman alive. Therefore you can takeover a Borg Cube and have the Borg Cube and the Enterprise-E at the mere cost of about a thousand members of your crew.
In Stronghold Crusader, you can set enemy buildings on fire (provided they aren't made of stone). Even better, the fire spreads, potentially turning the entire castle into a raging inferno. Aside from the cathartic potential, this is also an effective tactic, as it pretty much obliterates their economy and prevents them from replacing their troops. Of course, you may want to make sure the fire spreads, by taking out the water pots or killing the firemen...
There are also "Bad Things", ominous decorations (e.g. heads on a spike) and various forms of torture devices you can build in your castle to "encourage" your peasants to work and move faster; after a certain number is reached you can see peasants being tortured on them and when clicked on the peasants will cower and beg. They have downsides however: First, your troops take a penalty in combat (bad if you face opponents that build Good Things which gives them a combat bonus); and second, creates unhappiness which needs to be compensated in some other way.
The PC and Amiga game Syndicate, where evil corporations use squads of cyborg hitmen to duke it out in bloody campaigns of espionage and terrorism, and where plenty of innocent civilians would end up getting caught in the crossfire even if you weren't aiming for them on purpose (and let's be honest, you probably were. Maybe you even have brought the flamethrower for that reason.) And if that wasn't cruel enough, you could even use mind-control devices to round up herds of civilians and use them as meatshields.
Why use them as mere meat-shields, when you could arm them all with miniguns, or - god forbid - gauss guns. (Of course, if you wanted to be really cruel to your mindless minions, you could lead them on to a train track or other soon-to-be fatal area.)
Is it a subversion that the persuadertron (the Mind-Control Device) would let you take over and own the enemy agents without firing a shot, provided you first took over a large enough number of civilians?
That one is probably closer to Mercy Rewarded, as the persuaded agents get a permanent spot on your team if there's a vacancy.
The Total War series: there's just something darkly satisfying about ordering a cavalry charge or artillery bombardment and watching the enemy's levies literally fly through the air.
Ufo Aftershock: Your small band of Laputians are initially badly outgunned by almost every enemy you face. Luckily there are some Earth-based factions (Humans, Cyborgs and Psionics) who aren't going to attack you on sight. So it's a cruel but effective tactic to bring knives and look for missions where you help a faction against invaders. These faction defenders are heavily armed and can usually beat the enemy by themselves. So when the enemy is defeated, you can knife your "allies" until they fall unconscious. While unconscious you can help yourself to their equipment other than armor, they're also dying from all those knife wounds, so you can mitigate your conscience by saving them with a medkit. But even if you don't, your reputation barely takes a hit as casualties are assumed to be from enemy attack (your rep with a faction goes down far more if you hire someone and then fire them).
Countless Critters of several Warcraft games have met their bloody end at the hands of various troops.
or forum, you'll see the truly insane depths that this can sink to. In fact, there's an entire video series called "Things Crusader Kings Say