This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Metal Gear Solid 2: Sons of Liberty
In Metal Gear Solid 2 where Otacon's younger sister Emma dies. He cries and wails in misery, unable to focus on the mission at hand. Snake then fills his heart with courage once more in a brotherly embrace. As the two warriors leave the hacker, Emma's parrot mimics her, saying that she missed him, sending him once more into a tide of grief. The whole sequence is heartrending.
Not to mention Otacon has to decide to leave her corpse on the Big Shell, which is going to flood.
If Otacon wasn't The Woobie already, he damn sure is now.
Worse in the fact that Otacon, unlike most others in the series, was never a soldier or a fighter. He was just in the wrong place at the wrong time.
Any time Otacon cries is made even worse by the acting. Unlike almost any other performance, it actually sounds like someone breaking down. It's not a single tear, it's not controlled sobbing, it's wailing and screaming and crying like a child. Christopher Randolph puts everything into the scenes where he has to cry, and it is heartbreaking.
Even worse is the fact that her final request to be called by her birth name goes unfulfilled.
Emma: I remembered my brother giving me a piggyback ride. I was sleeping with my ear against his back. I could hear his heartbeat.
Raiden: Sounds like you two were close.
Emma: We were... back then.
It also doesn't help the fact that Emma and Otacon hadn't seen each other in years, and then when he finally sees her again, she is stabbed by Vamp just before she reaches him and dies in his arms.
Raiden: What if I've never really met her...? If the Colonel is something that I partly dreamt up, then... everything I remember about her could be...
Raiden's life in a nutshell. Forced to be Child Soldier and learn how to kill by Solidus, ended up taken in by The Patriots and later learn in-game that his life is just a fabrication, controlled by unknown conspirator like a puppet.
Olga's story is pretty sad. The Patriots took her newborn and forced her to secretly take down her comrades in order to help Raiden survive, otherwise they'd kill the baby, even at the cost of her own life. Luckily, Snake goes to save the baby after Solidus is defeated, and by five years later, he and Otacon have raised her themselves.
Fortune has also proven to be QUITE the tragic figure; perhaps the MOST tragic villain from the entire Metal Gear series, as she's never found any form of retribution, nor any signs of hope. The woman's lost nearly everyone she's ever loved, and can't join them in death. For Helena Dolph Jackson, her tragedy began since the death of her father (made more tragic considering the way she respected him as a soldier, not knowing the man was cheating on his wife/her mother), followed by her husband being thrown in prison for crimes he didn't commit, where he later died. Then, her mother committed suicide afterwards; but the final nail on the coffin is when Fortune suffers a miscarriage with her unborn baby. Losses like those would drive anyone insane enough to try to take on the world.
Nearly every scene with her it it can make even the most hardened of players look at her with pity. It's clear that she despises war, and at every turn, she's wishing for death, only to be endlessly disappointed.
The scene where a bullet meant for her hits Vamp instead, the closest she's ever had to a friend, and even a possible lover. The way she sobs and mourns shows just how much she's seen death, and wishes for the torture to end.
When it's revealed that nearly everything she's fought for was a lie, and that she's been played by the very people responsible for her current predicament, it's slightly gut wrenching to hear her cry in disbelief while slowly dying from Ocelot's gunshot wound.
At least Olga died with hopes that her child would be safe. The same can't be said for Fortune, since she no longer has anyone to lose, as she thinks Vamp is dead.
Solidus. Sure, you're a merciless former warlord who used child soldiers to wage war - just like dear old Dad - but your entire existence has been predetermined by people you've likely never met, don't know, and who handed you down orders from on high. They made you a monster. They determined that you - a Son of Big Boss, the supposed masterpiece of Les Enfants Terrible - would be that murderer, that warlord, that you would be President of the supposed free world. And when you realise all this, when you wanted to determine your own fate and break away from their designs for you... You eventually find out that they've planned even that, and used your own revolution to make an example of you.