This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Metal Gear Solid: Peace Walker
"I killed her... My beloved... With my own hands."
Strangelove's reaction to the above, one of distressed denial. She goes from hating Snake, to not hating him, to pleading, anything to try and get an answer to the Boss' death that would give it some kind of meaning. But there is none.
The game's theme songHeaven's Divide really tugs at the heart with just the instrumentals. Especially so if you pay attention to the lyrics.
There's also Koi No Yokushiryoku (Love Deterrence), Paz's theme which plays during the fight with her.
Some of Paz's diary entries.
And her final entry especially. Just as Paz was getting ready to enjoy a day of peace with the whole of MSF after Becoming the Mask, even playing the singing role for a band, Snake and others realize she's the Cipher spy and force her to act fast to complete her mission even though she doesn't want to. She even spares Chico despite the fact that he could've compromised her attempts to sabotage ZEKE, despite knowing full well it'd mean absolutely no benefit for her to let him live.
At the end of Chapter 4, when the mammal pod AI acts out the will of the Boss and drowns itself rather than have the United States launch a nuclear strike, all while singing THIS.
The entire final Peace Walker battles. Think shooting The Boss was hard in MGS3? This ending has an electronic replica of her sacrificing itself (AGAIN), and you're forced to tear her AI pod apart piece by piece while listening to her slowly dying from it.
And when that doesn't stop the signal Snake really starts to lose it as he continues to rip apart the insides. Snake's tone during all of this is reduced that of a man running out of options desperately trying to keep himself from cracking under the pressure of the situation. Especially so when he gags as if about to break down in tears out of sheer despair. There's even a quick time event here so the player can join in on Snake's futile banging on what's left of the pod demanding answers from the AI he just destroyed.
There's also the fact that while it does this, Big Boss unties The Boss' bandana and lets it fly into the sea with it.
I think what makes it worse, what makes it sting is that Big Boss finally accepts his title only while denouncing the Boss. It's really painful to see him basically accept his title out of little more than spite, and not fully understanding her motives. And because we've already seen his death, we know that he'll never fully understand for over forty years.
It's surprising that EVA's letter didn't make on it here.
Really, just when thought The Boss couldn't get any more tragic. She was screwed by her country at every turn, yet her loyalty to her country never wavered.
Euthanizing the Boss's horse the exact same way you killed her in Metal Gear Solid 3 deserves to be here.
Strangelove's last Memory Tape. The way her voice cracks as she breaks down at the end is heartbreaking.
Strangelove's Simulation, and more generally her obsession with creating an AI based on the Boss. In the simulation, she posits several scenarios while the AI reacts to them, and she uses this to try to find out why the Boss defected and why she allegedly nuked a Soviet research facility. The AI knows nothing more than what Strangelove programmed it to know, yet she desperately hounds it for answers.
The main point of the game: the world is in peace because we are pointing weapons of mass destruction at each other. Morbid.
The dialog which is also used as the opening for TGS 2009 trailer. Also an awesome accomplishment for the writers who manages to convey how utterly horrifying the idea of nuclear deterrence is in just a few sentences;
"You're crossing a suspension bridge. The bridge is only wide enough for only one person to pass at a time. A man is approaching from the opposite side. He's carrying a gun."
There's also Strangelove's increasingly pained observation as the mammal AI drowns itself that the Boss realized that there's no peace to be found anywhere. And that all people could hope for is the illusion that they call "peace."