This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Metal Gear Rising: Revengeance
The Jetstream DLC ending. The content itself doesn't hurt, but when you listen to "The Only Thing I Know For Real" again... everything starts to make sense about Sam's character. Fridge Brilliance and Fridge Horror kicks in a lot when you look over "Collective Consciousness" and Armstrong's cutscenes.
When Armstrong extends his hand toward Sam and welcomes him to the team, Sam looks down and starts laughing... but the way his shoulders shake and his facial expression makes it look like he's weeping because he just had the last bit of hope crushed from him.
There's something about the way Bladewolf pleads for you to stop attacking him just before you finish him off in his battle. He barely has his own life, but he doesn't want Raiden to take it away. Thankfully, Raiden has Doktor fix him up later on.
Talk to Courtney enough times and Raiden will lament on how his civilian life didn't work out the way he had hoped.
Raiden: There was a time when I wore artificial skin, tried to look as close to normal as possible. I've still got some now - on my face. The tech at the time wasn't great. You still looked pretty unnatural. Maybe you could fool someone from far away, but up close even a baby could tell I wasn't human. Going out shopping, or whatever... You could feel all those eyes on you. I tried to find something to do other than fight... But looking like I did got me two strikes pretty much as soon as I walked through the door.
Raiden: ...I'm a cyborg, Courtney. What am I gonna do? Drive an ice cream truck? I can pass as normal from a distance, but up close anyone can tell it's artificial skin. Good jobs aren't easy to come by these days, even for non-cyborgs, and I've got a family to feed. Besides... I've been fighting my whole life. ...It's just who I am.
Call Boris after getting Ripper Mode. Despite being in this form, Raiden, with much sadness and regret, will speak of his trying to put his bloody past behind him after the Liberian Civil War - and similar to the above not working so well.
It Has to Be This Way is far more tragic of a song when you realize it could apply to every game in the series, which basically means that after all this time, nothing has changed. Compare the number of casualties you'll realize that the only thing that's really changed is the technology used to fight each war, but the alternative is usually far worse. It really does have to be this way.
The tragedy of It Has to Be This Way is compounded by the fact that, barring a minor miracle, the Metal Gear franchise is effectively dead. After everything Big Boss, Ocelot, Snake and countless others suffered through over the years, all that's changed is The Patriots are gone. People still kill each other over things they don't believe in, causes that aren't their own. This is where the Metal Gear timeline ends. Square one with bigger guns on all sides.