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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.
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.