Any of those instances where you pause for a moment and contemplate the purpose of war as a young man in his prime is gunned down by enemy fire in front of you.
The ending movie of the first Call of Duty.
This troper was getting really into the Stalingrad levels, to the point of feeling immensely sad during the "Red Square" sequence and simply crouching behind the fountain in horror as all his comrades were cut down by the machinegun fire.
Call of Duty 2
Vic's death in Big Red One. If you've played this game, you'll know why.
Call of Duty 3
The penultimate level for the 1st Polish Tank Division in Call of Duty 3 ("The Mace"). Facing relentless German attacks, your tank is soon disabled and you're forced to fight on foot. Then, your companions are killed one by one as the defenses collapse one after another. Finally, just when all hope seems lost, green flares pop in the sky and Canadian reinforcements arrive. What made it so tear-jerking for the troper, however, was the knowledge that all this was faithful to real history. The Poles really did give their all in that battle.
"... Why aren't there any flares?" A crystallized shard of pure horror formed in this troper's gut when the Polish CO suddenly realized and shuddered: "It's _not the Canadians_!" Followed by tears when the CO later screamed in pure delight "GREEEEEN FLAAAAAAAARES!" when the Canadians finally got there. The emotional rollercoaster of that level was awesome.
The whole moment happens quite suddenly, but this troper was rather moved by Pvt. Chernov's death in Call of Duty: World At War. To put things in perspective, throughout the game, Chernov was the only member of the Russian squad to show any kind of restraint in battle, loudly chastising his comrades for their brutality; his cries always fell on deaf ears. Right at the beginning of his last level, Reznov loudly scolds him for his "lack of stomach" and makes fun of him for keeping a diary. At the end, the poor guy gets deep-fried by an SS trooper with a flamethrower, and as he lies in agony, gasping for breath, Reznov seems to have a change of heart and comforts him in his last moments. He then takes his diary and remarks, "Someone should read this..."
I found it much worse when Sgt Roebuck dies. I saw him get grabbed by that soldier and just couldn't save him. I just kept thinking that "it wasn't my fault, I couldn't save him". It doesn't help that later I found out that you could let Polonsky die instead, but I don't want to play that level again.
The emotional feel of the game is ruined for This Troper if you let Roebuck live, even though he is a total badass and Polonsky is a whiny twit, although he matures when Roebuck is killed.
Polonsky: "Those fucking animals, they killed him! You're all going straight to hell, ya hear me? Straight to fucking hell!"
In the same game, the ending, when Reznov helps you up to plant the flag on the Reichstag.
I cried when Reznov helped me, but they weren't tears of sadness. They were tears of happiness, because Reznov loves Dimitri enough to brutally murder the Nazi who attacked him and help him up to claim the honor he deserves.
World At War's ending. After having fun shooting Nazis and helping the Red Army win, General Macarthur's speech pulls you out of the game's escapism to remind us of the dark reality of war; it affects us all.
General Macarthur: "We are gathered here, representatives of the major warring powers, to conclude a solemn agreement, whereby peace may be restored. It is my earnest hope, and indeed the hope of all mankind, that from this solemn occassion, a better world shall emerge out of the blood and carnage of the past. A world founded upon faith and understanding, of man and the fulfillment of his most cherished wish, of freedom, tolerance, and justice."
After this footage, there are two stark sentences displayed before the end credits:
60 MILLION LIVES WERE LOST AS A RESULT OF WORLD WAR TWO.
IT WAS THE MOST DESTRUCTIVE AND DEADLY CONFLICT IN HUMAN HISTORY.
In World at War, The opening of "Vendetta" the first Russian mission in the game. What happens is you're laying in the Red fountain, watching as your follow comrades are being killed by Nazi soldiers. The Music doesn't help whatsoever.
Call of Duty: Black Ops has the death of Dimitri Petrenko in Project Nova. Long story short, the antagonist, Soviet General Dragovich, decides to test his newly acquired Nova 6 gas on his own men. Unlike the aforementioned Shepherd, he doesn't even have the excuse of tying up loose ends - he just does it because he has something against Reznov. It's not even a quick death - you watch him suffocate and vomit as his skin burns, while he's banging uselessly on the glass door between your cells. The fact that the usually hamtastic Reznov is recounting this in a completely downbeat, despairing tone does not help.
Dimitri: 'You should have died in Berlin.'
Looks like death doesn't like to be cheated.
The ending of Vorkuta, when it becomes clear only Mason can make the jump onto the train.
One of the sadder moments of the game comes in a bombed-out garage in the Hue City level. It's not even a cinematic, but if you glance around at the dead Vietnamese, you'll see a man kneeling by one of the corpses, attempting to perform CPR. After about ten seconds of this, he sits up and sobs hopelessly into his hands before trying desperately to revive his dead friend once more. And you can't even comfort the poor guy.
Black Ops seems to end in a high note. Mason shrugs off the brainwashing, the attack on America was stopped, and the bad guys are all punished. Then you read the unlocked intel pages, only to find that Mason never fully recovered, and because of that he was finally considered a threat to national security by the CIA and marked for termination, along with Hudson and Weaver. They escape to South Africa, and the last thing we know is that joint operation between the CIA and MI6 is being prepared in order to assasinate the three heroes that saved America. This is extra sad considering Reznov's words on being betrayed by your own. This is made even worse by the fact that one of the "betrayers" might be Captain Price or MacMillan, two of the most popular characters from the Modern Warfare series. Talk about your conflicts of interest.
Although, in Black Ops 2, assuming you didn't shoot Mason (disguised as Menendez with a bag over his head) in the head, he survives to the age of 93, and even goes to the Vault to meet up with his old friend Woods. A dose of Crowning Moment of Heartwarming comes when the two even start bantering like old times.
Farid executing Harper to maintain his cover as a CIA agent. Made worse by Harper screaming at him to "do your job!" while Farid holds a gun to his head, and then even more so when - even when Section arrives seconds too late and tells Farid that it's okay, that he did what he had to do - the camera shows Farid broken and in a state of shock at having killed Harper.
Farid is screwed either way. He can kill one of his best friends, or he can try to shoot Menendez. In the latter option, Menendez dodges the gun, shoots farid in the stomach, rants for a bit, and then executes him. Poor guy...
Farid dies in most of the endings, either by failing to kill Menendez, or trying to stop Salazar from shooting Karma/Chloe.
When Woods is ordered to shoot an assassination target, only to find out he was tricked into shooting Alex Mason. Then we see young David Mason's reaction when he sees his father lying in a pool of his own blood, presumably dead. The music that plays as you run up to Mason's body perfectly captures Woods' Oh, Crap moment as he realizes what he just did.
Also Hudson sacrificing himself to save David and Woods. As Menendez is counting down to when he blows David away, Hudson is madly and tearfully begging Menendez to kill him instead and dies a horrible death as a result
Menendez failing to rescue his sister, and then seeing the grenade explode in her room.
Everything about Josefina counts, if only to remind you that Raul Menendez loved his sister more than anything in the world. The masks on the wall always stand out, as if he wanted to protect her from her ugliness. And the terrified, desperate wailing she makes when she's dragged out of bed? Borders on Nightmare Fuel...
Wood's death if Karma is dead and Menendez is spared. Menendez infiltrates the Vault, kills Woods with Josefina's locket, and lays him down gently on his bed. Very slightly dulled, considering Woods is currently 95, and doesn't seem too phased by Menendez appearing in his room.
Salazar's betrayal and subsequent death, if Harper is alive. The guy's been with you in all of the 2025 missions, and is actually a decently coded teammate that helps you push forward on his own if left alone. And he turns out to be in league with Menendez, and through his actions, allows the US Army's drones loose on China and America, causing countless deaths. But unlike your typical traitor in the genre, Slazar allows himself to be arrested and is willing to receive the punishment for his actions from his friends
Mendendez's suicide in the "worst" ending is a twisted example. After escaping from prison and killing Woods, he goes to his sister's grave, digs her up, smashes open her coffin and calmly pours gasoline over himself. Then, while looking at her remains... he lights a match. It's a poignant yet chilling way to depict a character that was so utterly consumed with vengeance that once he achieved it, he had nothing else to live for. So he decides to end his own life, and be with his sister.
In the same token that it's a heartwarming moment, Mason having to tell his son he's duty-bound to save Woods is a sad moment as well. Alex really doesn't want to break the promise he made to his son that he put his military life behind him and David is also disgusted that his father is going back on his word. It's not a comfortable moment for either party.
Admiral Briggs' death and the subsequent destruction of the Obama. Made worse by the fact that he's killed by Menendez...except you're controlling him at that moment, meaning it's entirely your fault.
The ending once you view the after credit stinger, sadistically subverting what was supposed to be a happy ending. Despite shooting Gabriel Rorke in the chest and leaving him to drown in a lake, he rises from the waters, kicks Hesh Walker in the guts and gloats about how he's going to turn Logan against his brother and the Ghosts, dragging him off while Hesh screams desperately, utterly helpless to stop the madman. The last shot is of the player trapped in a pit in the Amazon being tortured into becoming loyal to the federation