This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Metal Gear Solid 3: Snake Eater
"Jack... Or should I say... Snake... You're a wonderful man."
The End's last words and death.
The ending of of the whole game and the death of The Boss was a very intentional example designed to show Naked Snake, aka Big Boss'Start of Darkness. When she is defeated and asks Snake to kill her, he aims a gun at her heart and the game waits for you to press the fire button. After spending the entire game hearing about and seeing traces of the intense bond that Snake shares with her, it is quite possibly the biggest Player Punch in the entire series.
And the later revelation that The Boss was a Fake Defector committing what she knew to be a Suicide Mission at the sacrifice of her honor for all time. One of the greatest heroes in American history will forever be regarded as one of the worst traitors. The last scene of the game is punctuated by the now-iconic image of Naked Snake's salute◊. There's a reason the image is the one highlighting the Tear Jerker page for the series as a whole.
You don't see EVA's face for any of the last portion of the ending scene, but you hear her start to break down and sob. Listening to her voice cracking on the last part of her voiceover, coupled with the visual on-screen at that moment, makes it very hard to not get choked up along with her. The line where she chokes up doesn't help:
EVA: Snake... the world will never know what she did. She was a real hero... She was a true patriot.
The flower petals in The Boss' death scene were extremely poignant, especially considering the different cultural connotations of the color white. In Western culture, white symbolizes purity and innocence, and is worn by the bride at weddings. In Eastern culture, it symbolizes death, and is worn at funerals. Red is also subject to such duality. Western culture views red as bloody and impure, while Eastern culture views it as a color of celebration. So the petals turning from white to red actually has two meanings: the first is that it symbolizes Naked Snake's loss of innocence as he inherits the title of "Boss" and becomes Big Boss; the second being that while The Boss' death is sad, she's moved on to a better place and is reunited with The Sorrow.
The Boss' headstone has to leave her name out, with only "IN MEMORY OF A PATRIOT WHO SAVED THE WORLD 192X-1964" written on it.
Another thing related to the flower petal turning white from red. Before the fight with her, the Boss said something along the lines of how her blood turned as white as snow while she was in Nevada. Red to white. Make what you will of it.
The song "Way to Fall," which plays during the credits, is a very sad song, especially because the lyrics go so well with The Boss' death and how Big Boss feels.
Son, you've got a way to fall, They'll tell you where to go, But they won't know... Son, you'd better take it all, They'll tell you what they know, But they won't show... Ohhhhhh... I've got something in my throat... I need to be alone... While I suffer...
The "Snake Eater" song too. Despite being surprisingly fun and upbeat, the song also foreshadows many events in the game including the demise of The Boss.
There's something about The Fury's last words, especially the melancholic delivery, that are incredibly touching:
The Fury: Mission Control, do you read me? I'm coming home!
At the beginning of the game when Snake and the Boss have their Codec conversation. When you know all of what is about to happen, there is something heartbreaking about hearing Snake say, "it's good to hear your voice again."
The Boss' speech before the fight against her, where she gives her backstory and a deeper understanding of her motivations. Even before finding out she's a Fake Defector, all of your thoughts that she's anything but a good woman should disappear at that point. Only making the fight against her and its aftermath more gutwrenching.
Snake not uttering a word during his debriefing at the end, being too heartbroken over the information EVA revealed in her tape to even speak. As he leaves without saying anything, Para-Medic is visibly concerned.