Mass Effect 3 is built around this trope. When you see a soldier both frustrated and heartbroken over a woman who keeps inquiring about her son, you'll understand why.
From the very beginning, as the Reapers are laying waste to Earth cities, you rescue a young boy and put him on an evacuation shuttle, only to watch as a Reaper calmly blows it out of the sky. For the rest of the game, Shepard is haunted by nightmares of the boy being consumed by fire.
The Metal Gear series is about many things, but its most fundamental theme is that there's nothing glorious about war, and everyone involved suffers a lot, one way or another. It does so by playing its tropes so straight they end up deconstructing themselves once they get to where they're going; Child Soldiers, for example.
Metal Gear Solid 3: Snake Eater is an unflinching look at war and what it does to its soldiers. The Big Boss is forced to assassinate The Boss, the greatest hero of World War II and the single most important person in his life, all because factions of the Philosophers are fighting over money. The core message is that there is no such thing as an enemy in absolute terms, and that our allies today might be our enemies tomorrow. This is because our enemies are human beings, just like us. The game hammers that point home with the subtlety of an anvil, but it's a very effective message.
Metal Gear Solid 4: Guns of the Patriots shows how bad things can get if war isn't Hell. The nanomachines inside people suppress the psychological and physical stress that brutal warfare normally inflicts on them, and the entire world has become engulfed in a pointless War for Fun and Profit. When the system goes off-line for good, all the soldiers in the world collapse and become sobbing wrecks as the trauma the nanomachines suppressed catches up to them.
Considering the depravity and inhumane cruelty his enemies display, this is arguably justified.
Fallout has a famous quote that starts "War... war never changes." that paints war as an indelible curse of mankind. See the quotes page for the full version.
Call of Duty lately has been sporting a coat of anti-war paint with some of its quotes. Ever knew how much a Tomahawk missile cost? War ain't cheap.
We get a second coat of Call of Duty anti-warpaint in the Modern Warfare series. Fancy dying in the Middle East from a nuclear explosion? How about you and your unit being killed so close to completing your objective? Or infiltrating a terrorist cell for the CIA where you have to gun down people at airports, before being killed as a spy? Or the world entering a third world war and you being branded a traitor for killing the people responsible?
Even Fire Emblem uses this trope, especially in Radiant Dawn when the war causes the Tellian equivalent of the Apocalypse.
Awakening somehow manages to play this straight and for for laughs at the same time. Sociopathic dark mage Henry is a former soldier for Plegia, who your party just fought in a war. So naturally, child soldier Ricken is curious about how Henry feels about fighting alongside those who killed his former allies. Cue Ricken falling into a depression while Henry happily talks about the (suddenly less sinister) bosses you fought:
Ricken: Remember a while ago, when you told me that you served under Gangrel? It made me wonder... Have you fought against anyone you knew?
Henry: Yeah, sure! You've cut down a few of my former comrades. You interested in who they were? Lemme see if I can recall... Well, there's Vasto. I liked him! Always ready with a joke or quip.
Ricken: That guy?! He tried to stop us when we headed east that one time.
Henry: He was really excited about that posting—it was his first major command. Ha! He used to talk about his mother all the time. "Best knitter in Plegia," he'd say!
Ricken: Oh. That's...nice.
Henry: Then there was Mustafa. He always gave me a bag of peaches whenever I visited. He said I reminded him of his son and that I should consider myself part of his family.
Henry: Oh! And Campari used to make little birdhouses for homeless—
Ricken: Actually, Henry? I don't think I want to know about your comrades after all.
Henry: Aw! I thought you were interested.
Ricken: I was, but now everyone seems more...normal than I expected. They're not maniacs or monsters. They're just like us, except they're dead.
Henry: Yep. Dead as driftwood, they are. And it was you Shepherds who killed 'em! Their friends and families are probably still crying their eyes out.
Henry: What's wrong?
Ricken: Henry, it's my job to kill Plegian soldiers... So I have to believe they deserve to die. But now you've reminded me that they aren't faceless blobs with axes. They have friends, and families, and... H-how am I going to fight them if I know that? What if I hesitate?
Henry: You're weird. I don't see the problem here at all.
Killer7 - Word of God states that one of the messages of the otherwise unfathomable Killer7 is about the futile, cyclic nature of war. Emphasized by the ending: the entire conflict between Harman and Kunlan is nothing but a game meant to help the two immortals pass the time. The two have even switched roles.
Skyrim has this in spades. One NPC mentions that there are no innocents, only the guilty and the dead.
Demonstrated by the town of Noringia, which has been heavily bombed and looted by Tierran forces, should you explore the town, you see that starvation and poverty is rampant amoung the refugees still living there.
In the final battle, If you successfully repel the Antari assault, the aftermath shows you surrounded by the corpses of the majority of your men, possibly including your Staff Sergeant, and most of the survivors badly wounded, at that point, a horribly maimed Cazarosta suggests piling the corpses into a makeshift barricade to repel the next attack, War Is Hell indeed.
The Gears of WarExpanded Universe had local big dude Tai, upon finding his village razed to the ground, remarking that, "Some people have said 'War is Hell.' War is not Hell, for in Hell, innocence is spared."
Lost Odyssey, when a completely immortal guy has lived for 1000 years just to see mortal people killing each other in war, you can really feel how much it makes him want to be freed from it. Yet he can't.
The Brothers in Arms series started with a fairly strong anti-war message and has been gaining in intensity since then. Hell's Highway is particularly not only kills off or maims established characters, but depicts PTSD (sometimes in frightening ways.)
Leggett: Well, this looks familiar.
Halo - While they were serious from the start, it wasn't until the third game it became clear that this is the main aesop. Yes lovable main characters were killed in the first game, and the second game became more uglier about the situation, but that was out-shadowed by awesome playstyle, story, weapons and a badass player character. But by the time of third game, all of that were thrown right out of the window. Halo3 was not afraid to show how shitty a three-sided war between Humanity, a galactic empire made of genocidal, fanatical aliens and a parasitic species of undead monsterswould be; Anyone can (and will) die, even main characters as Sgt. Johnson, Miranda Keyes, 343 Guilty Spark, Prophet of Truth, etc, cities are burned to the ground, billions are killed, even the most Ineffectual SympatheticMooks become ferocious, bloodthirstywarriors after they had been through wars long enough, people suffers from psychological damages of the whole thing, and not just biological creatures but also supposedly unliving machines such as Cortana (whose torture at the hands of Gravemind almost breaks her into a depressive Empty Shell), 343 Guilty Spark (whose isolation for the last 100,000 years and status as the canon scrappy becomes to much for him to handle and snaps into a dangerous killing machine), and Mendicant Bias (whose 100,000 years of overwhelming guilt because of his treason against the Forerunners cause him to sacrifice himself to help Master Chief), and Master Chief, The Hero of the story, ends up in no-ending space without any way to get back to Earth. Plus that great civilization that was destroyed due to the 300 years war against the said undead monsters, which forced them to kill themselves in a massive sacrifice in a attempt to take their enemies with them — only it was All for Nothing.
Halo Reach. All the other main games had the knowledge of the Halo rings as hope, or at the very least a game changer, not the same old stalling against an unstoppable more technologically advanced horde of intergalactic aliens who deem your entire people heretical. Halo Reach is that, each subsequent mission just makes it more and more clear that despite Reach being the most advanced colony and the one with the greatest military presence it will still repeat the same fate of its bretheren, and all you are doing is trying to save the most people you can/and or kill the most Covenant. The last two missions you do in a way find out about the rings, and you give it your all and sacrifice almost of Noble Team (meaningful name) to take it on the last transport leaving Reach. Yay you did it, all those missions, all those kills, all the obstacles passed by a hairline, now you get your long deserved reward right? Except somebody needs to fire the gun. You are left on Reach, with scattered unorganized resistance as its being glassed. And no matter how hard you fight, you will die. Halo Reach is game that shows that even if you give your all and be a good soldier, hope is not guaranteed.
The backstory of the franchise takes this to Cosmic Horror levels. The Flood is a direct consequence of war being the vengeful remnants of Abusive Precursors who were slaughtered by the Forerunners.
Of course, in Halo Wars Spartan Red Team tries to make this trope work for them:
Final Fantasy Type-0 pulls no punches in showing how horrific and brutal war can be right from the start.
Its opening cinematic features the graphic death of Izana Kunagiri and his war chocobo from injuries as Ace, Queen and Jack stand helplessly (and all Ace can do is weep for him). There isn't much that could make war seem less glorious than showing Machina's older brother reduced to the level of complete freakout from his pain and fear of dying.
Then it goes downhill from there... on all four sides of the war. In Rubrum thousands died (including all of Class Zero save Machina and Rem), and the ending reveals that the entire nation was left ravaged and would only recover after at least fifty years under Machina and Rem's guidance. On Milites thousands of soldiers and mechs died serving a charismatic leader who was Dead All Along, possessed by an Omnicidal Maniac, including those reduced to Phantoma by Alexander, the summoning of which required theHeroic Sacrifice of hundreds of Rubrum cadets, as well as instructor Kurasame Susaya and Alexander's main summoner, Caetuna. Lorica was totally destroyed, its king, Gilgamesh, left to wander Oriense without a purpose in life. Concordia was shaken by its queen's death, and the revelation that its (mostly ceremonial) king, long scheming for a return to a patriarchal rule, had a hand in it.
War is always the main theme of the Suikoden series. Many characters get involved in different wars, and more often than not they end up traumatized in a way or another.
Suikoden II has a character named Pilika, a sweet and joyful little girl, who, in rapid succession, lost her hometown, her whole family, and nearly her own life at the hands of Luca Blight, an Ax-Crazy prince who enjoys butchering men and women like pigs. All Riou and Jowy could do was nuisance him a bit, get swept away with his sword, and watch helplessly as he was about to kill her, while Jowy could do nothing but yell helplessly at him to stop. They were saved at the last second by an explosion caused by your allies, and escaped during the confusion. However, this last event finally break the mind of Pilika, making her mute for nearly the entire game.
Homefront portrays war as savage, brutal, and inhumane affair where good people die for no reason, as well as driving home just how easy and potentially horrific friendly fire incidents can be in one of its more intense and memorable sequences. It also makes the point that, as horrible as war is, sometimes there really isn't a better option.
In the simulation game Afterlife (or rather "Hell Is War"), the most advanced hell building for the wrathful is a war where the damned are forced to fight endless battles, and if they are killed their bodies are regenerated and sent to fight again and again.
In Knights of the Old Republic II: The Sith Lords, it is shown that the war in the previous game has had absolutely devastating consequences for the Republic. Most of the playable characters, including the protagonist, are Shell Shocked Veterans who have lost family, friends, limbs, and sense of self. Throughout the game you meet refugees, embittered ex-soldiers, and traverse planets that are still physically and culturally ravaged five years after the war's end while the galactic government collapses slowly.
Eternal Darkness features a chapter set in a Creepy Cathedral used as a field hospital in Amiens, France, during the Battle of the Somme, with all the gruesome sights and sombre atmosphere that one might expect of such a setting. It is even implied that Pius and his acolytes manipulated events towards the war just so that there would be more death to harvest. Mind, given that this is a Lovecraftian horror story, there are far more horrific things than war in the cathedral...
Spec Ops: The Line: The protagonist and his men become increasingly violent, unstable and shell-shocked as the story progresses. It doesn't help that both sides of the conflict, the CIA and the Damned 33rd Infantry Battalion, are busy killing each other - and civilians - in a hopeless struggle to reassert some sort of order in Dubai's ruin. Later in the story, the Damned 33rd begin to use whitephosphorus on insurgents. The player then uses white phosphorus on a refugee camp, unknowingly. The CIA blows up the city's only water supply, dooming everyone in order to keep the world from learning about what happened in Dubai. Nobody comes out of the story looking good. Or sane. Or, in some endings, at all. The worst part is that the situation didn't have to escalate that far. The main reason it did is because Walker, and by extension the player, wanted to play hero. What makes this whole situation even more tragically senseless is that it isn't even set in a war. This is a simple recon mission gone horribly wrong. All Walker had to do was report on the situation and leave. Walker treating it like a war story and acting like a war hero anyway makes everything worse.
Far Cry as a series. Far Cry 2 has you hunting the Jackal, who understands that the geopolitics of Darkest Africa make it impossible for any meaningful peace to be made there, and trying to fight back against this fact will simply see you consumed by the same violence yourself. In Far Cry 3, your character begins as a young adult who's never fired a gun outside of a shooting range, desperately scrambling to survive. In the end he's approaching the same threshold of madness crossed by the villains, reveling in bloodshed and obviously suffering violent psychotic episodes.
This manifests as an entire realm of the netherworld in Folklore called Warcadia, a place built from humanity's contemporary fear of death, where people go who died suddenly or without explanation end up. The place is under a constant state of warfare without reason or any possible outcome. This is quite literally meant to be a hell of unending battle.
In the backstory to Another Code, both of the Edwards brothers got drafted into World War II. Henry manged to recover despite losing an arm, but Thomas turned into a Shell-Shocked Veteran and lost his trust in others, setting up in the tragedies that would befall the Edwards family.
The snippets of story that accompany Armor Alley emphasize this theme.
I don't recognize any of the guys I'm with here, and I don't know if it's because they're green troops and all my friends are dead, or because I'm losing my mind.
While the Vietcong series doesn't demonize war, its hard difficulty, not to mention its focus on realism screams this trope at the top of its metaphorical lungs.
It is stated often and sometimes shown in Tears To Tiara 2. Hamil considered accepting the enslavement of his entire people to avoid war. Saul was willing to let slide agents from The Empire buying slaves and dead bodies to prevent war. Until Hamil points out to him that he's only prolonging the inevitable, which he knew, and said agents took Artio which would cause war to erupt anyway.
Iji features a Mêlée à Trois between the title character representing the last surviving humans on Earth, the invading Tasen, and the genocidal Komato, who the Tasen invaded Earth to run from. There are complicated sympathetic characters (who aren't immune to plot-related death) on the latter two sides even though they're both the enemy, and trying to solve the situation with violence means the player can watch Iji slowly break over the course of the game, going from shakily apologizing every time she kills to practically turning into a full-on berserker. It also manages to avoid the Do Not Do This Cool Thing cognitive dissonance that some Call of Duty ripoffs have, as well as the But Thou Must hypocrisy that Spec Ops: The Line's white phosphorous scene was hit with, by letting the player go through the game without (technically) killing anyone, and you end up with a slightly better ending for doing so.