The ending, in which Big Boss uses his much vaunted CQC techniques to disarm Snake and then give him a hug before telling how much he respects him as a man, then dies after sharing one last cigar with his son.
In spite of his claims that he never thought of David as a son, Big Boss's love for him as a father is all but confirmed with this:
Big Boss: Snake, you are free now... Don't waste it... Start a new life.
What makes it all the greater is Big Boss and Snake's Japanese voice actors are father and son in real life.
What makes it all even greater is that the two of them were estranged and distant before the game started development, and Kojima intentionally chose Big Boss's actor to get them to reconcile. And they did.
Made all the more heartbreaking for the fact that David has only SIX MONTHS left by that time.
The touching, soft music, the imagery and glowy haziness of all the white flowers in the cemetery, and Big Boss' "This is good, isn't it?" never fails to make players tear up.
And a short time before that, Big Boss delivers another heartwarming line while he perfectly sums up the lesson he learned from all the years of war (and at the same time makes clear that the saga finally has reached its end).
Even though EVA may not have believed David's father loved him, she freely admits that she always has.
Eva: I'm sorry. Your father never wanted you. Human life isn't meant to be manipulated like that. I knew that, but...I wanted you.
Also, when Snake lights Big Boss' last cigar. Snake performing a gesture of familiarity and friendship to his estranged father (whom he also tried to kill twice) is quite sweet in itself.
There's also Big Boss saluting The Boss' grave, which is also an understated Moment of Awesome. He's so weak, even sitting up is hard, but he stands at attention. His arm trembles as he tries to lift it, but as soon as his hand reaches his forehead, he forces himself to stop shaking and deliver a proper salute to the woman who defined his life.
Sunny forming a microcosm of the ideal of world peace when she says of her new friend, "We don't understand each other's language, but we're having fun."
Meryl and Johnny's wedding.
Meryl's rejection, promptly followed with a counter-proposal!
Something apparently overlooked: After GW goes down and the absence of the system leaves Outer Haven's unmanned defenses dead weight, it also leaves the FROGs as lumps of weeping, broken women from the onslaught of, until now, suppressed battlefield trauma. The ensuing montage includes a scene of the Missouri's Marines, although keeping their guns trained at all times, rescuing them, with the less debilitated FROGs in the rafts trying to comfort the ones who have lost the will to even move. One FROG even holds another who has collapsed while stroking her head.
Big Mama (AKA Eva) saying "That's my boy!". Now if that isn't a touching mother and son moment, nothing is.
Let's not forget Raiden's segment in the end of the game either. After suffering all kinds of injuries, emotional and physical, Raiden is fitted back with an organic-lookalike body and then reunited with Rose, who is accompanied by a little boy. She reveals that the child is Raiden's son and her apparent marriage to Colonel Campbell was just a cover to protect John from The Patriots. John tells Raiden he's cool like a superhero, and then flourishes his toy sword just like Raiden did in MGS2. The three of them embrace, Raiden promises Rose he will never abandon her again, and they finally get to be the family they always wanted to be. Say what you will about Raiden, but you can't deny that after all the crap he had gone through in his life, he really needed and deserved that happy ending.
In the celebratory moments after Meryl and Johnny's wedding, Campbell simply looks up to the heavens and says, "Thank you, Snake."
The scene in the act 5 briefing where Otacon pulls out his lighter and lights Snake's cigarette for him, despite berating him throughout all the games about his smokes, is oddly sweet.
Don't forget the final scene that played after the credits rolled. Otacon promises Snake that he will remain with him as a witness to his life, remembering everything that Snake ever was, and saying that he and Sunny will stick with him until the day Snake dies.
The most heart-rending line is "You don't have to come." And the most heartwarming is the fact that Otacon will not hear of it.
Also, how that scene starts. Otacon says that Snake forgot his cigarettes. His answer? "No, thanks, I'm quitting. Those things'll kill ya." After considering himself a dead man walking for the entire game, he's looking forward into a future where he lives, even if it isn't very long.
Psycho Mantis' utter glee when using a controller with Dual Shock 3 technology is oddly heartwarming. Yes, he killed a lot of people. Yes, he attempted to make Meryl blow her own brain out...in two different games. No, he wasn't sorry about any of it. But he got one last chance to have a little fun messing with your controller, and he's so happy about it he practically sounds like a kid in a candy store.
Doubly adorable since the poor thing tried to read your memory card like the old days in addition to the above, but failed thanks to the PS3 not using memory cards and sounded so dejected when he couldn't.
During the microwave corridor scene, the camera divides between Snake and all his allies struggling in a Last Stand of sorts, only for one divide to show Sunny's fortune eggs finally come out great for once, foreshadowing that things will be okay in the long run.
On the subject of Sunny, her presence by Snake and Otacon's side is pretty heartwarming when you remember the events of Sons of Liberty. In the end, Olga giving up just about everything wasn't all for nothing, after all.
"Just like your father... *hand gesture* You're pretty good!"
It's even better when you consider that his last words were the first compliment the man he loved ever gave to him.
The entire final battle with Liquid Ocelot counts as this in a way. It's the ultimate showdown between you and your greatest rival. One last enemy to be defeated. And by God does Liquid gives as good as he gets, so you might get quite a few of game overs. The kicker is that the word 'Exit' has been changed to 'Exist', and when you select it, you hear Liquid just screams "It's not over yet!" before giving you another chance to rethink your decision. That's right, the game itself doesn't want you to give up. You've come so far and overcome every odds that's been thrown at you (even moreso if you have played through all the previous games), and there's only one obstacle between you and the ending of the entire series. This is especially meaningful on harder difficulties, where you're sure to get A LOT of game overs fighting Liquid. And the way he tells you that it's not over could imply that deep down, he wants you to win. The Big Bad of the game wants you to win.
Even better, to remind you of everything you've gone through, the game will switch HUDs throughout phases of the battle, switching your health bars and the names of your characters to the heroes of old to make you remember just how much history is taking place and riding on you to win.
And of course Liquid wants you to win. Rather than letting the fight end at any point beforehand during the cutscene, both Liquid and Solid make the conscious decision to inject each other instead. Despite the rivalry, or perhaps because of it, they choose to continue their "final moment", one last time.
After defeating each member of the B&B Corps, Snake is told of their traumatic backstories by Drebin, and how their minds have been cleansed by their battles with him.
Even more heartwarming is if the player decides to have Snake spare them by shooting the poor girls with tranquilizers instead of killing them. They simply fall asleep peacefully while curled up in a ball. In particular, Laughing Octopus, the first of B&Bs you fight, doesn't just fall asleep. The mad laughter is replaced by the joyous laughter of a baby. As Snake checks her pulse, she can be heard calmly breathing in and out as she sleeps. This implies that they all had trouble sleeping at night, if they ever did sleep, thanks to their traumas, but now that they're put to sleep by Snake, the man they've been wanting to fight and kill this entire game, they can rest easy now.
Though Snake and Akiba initially start off on the wrong foot, Snake appears empathetic towards the latter's case of diarrhea. Akiba returns the favor when helping Snake to his feet during Liquid's hacking of SOP, with Snake being among those affected.
During Act 3, Akiba excitedly calls out to Snake
Though not seen in the game proper, and therefore dubiously canon, the Project Itoh novelization of the game mentions that, after the events of the story, the time Snake, or rather, David, had left with his life was spent happily. He travels the world with Otacon and Sunny to see life free from the Patriots, and shares his story so that future generations will know what he fought for. Ultimately, he passes away by peacefully falling asleepwith a smile on his face.
