Either ending. in the "good" ending where Meryl lives, Snake realizes he should live for the sake of others - specifically Meryl. He also reveals his real name, David, to Meryl. The "bad" ending is almost identical, except Meryl is replaced with Otacon.
The last scene in Metal Gear Solid (the bad ending, granted) when Snake and Otacon call each other by their real names for the first time. Aww...
Not only that, but they ride off together into the Sunset.
Snake choosing not to tell Naomi that Frank Jaegar killed her parents, knowing fully well what the truth would do to her.
To say Psycho Mantis is a sick fuck is a massive understatement... and yet, I couldn't help but find his death scene poignant, especially with his revealed backstory. "This is the first time I've used my powers... to help someone... strange... it feels kind of... nice..."
Also, Snake's talk with Sniper Wolf before giving her a Mercy Kill, assuring her that she's no dog of war, but a proud wolf.
Not killing any of the wolves because they really are noble animals and in honor of Sniper Wolf.
The comic adaptation changes her speech, and it's no less heartwarming - rather than depicting Otacon as being "in love" with her due to Stockholm Syndrome, they both instead show concern for each other and seem to genuinely like each other. She gets shot by Snake, and when Otacon starts to blame himself for it, she assures him that it wasn't his fault, and that she genuinely cared for him and felt that he'd shown her what true compassion was after so many years caring for nothing but killing people.
While planning the escape with Otacon and Meryl, Snake thanks Otacon for the first time in the game and tells him "I believe in you."
Let's put this in perspective: a hardened special ops soldier who's seen all the horrors of war, is telling a meekly nerd who's effectively been a hostage the whole game that he believes in him to save his life. Perhaps this is where Otacon started believing in the one who believed in him.
Similarly, in his final codec with the Colonel, Snake calls him "Roy" for the first time in the game.
Even earlier in a conversation with Naomi, Snake tells her that he considers Campbell one of his few friends, despite having just realized that Caompbell has been withholding information about the mission. Campbell's response is an earnest sigh of relief followed by "you're still calling me friend?" Even more poignant as in the mission briefing, Snake was skeptical when Campbell called himself an old friend of Snake's. Jerk with a Heart of Gold big time.
"Live Snake, that's all I can say to you."
Gray Fox's Obi-Wan Moment, where he takes a moment to reassure Snake that there's nothing wrong with the way either of them have spent their lives, and to wish him the best for the future.
Gray Fox: Snake, we're not tools of the government or anyone else. Fighting was the only thing... the only thing I was good at - but at least I always fought for what I believed in. Snake... farewell.