While most of the Cobras you fight as the game progresses are clearly mentally ill, you can't help but feel sorry for them. Special mention goes to The Fury, who in his final moments begs The Boss to have caution, so she can live longer, and says he's off to join The Sorrow, clearly showing deep feelings of friendship.
And after you fight The End, he thanks you for giving him a warrior's death.
After Naked Snake gets his eye shot out in Metal Gear Solid 3, EVA says, "I'll be your eyes from now on." She's hardly the most genuine character in the series, but in that moment, you know that her gratitude for his sacrifice to save her life is real.
Before the first stage of the boss fight against the Shagohod, Snake tells EVA that he trusts her to handle the driving so long as he can handle the fighting. A first-person view prompt shows up during this scene. Usually during scenes with EVA, Snake stares directly at her chest, but this time, he looks at her face, right before they kiss.
During the Cell sequence, try throwing your rations back at the guard. After three times, he'll be thankful that Snake shared his food with him, and will open up for a friendly chat. Not only does it turn out he's Johnny Sasaki's grandfather, but he's really homesick and lonely. He then goes on to show Snake a photo of his familynote (Has an emergency frequency number that unlocks the cells on the back), and returns Snake's cigarettesnote (Secretly a spy gadget that sprays anesthetic) for listening to his troubles.
While playing the game, we've been told that Tatyana is Sokolov's mistress. Sokolov says that he wants to be reunited with his family, so you think he's a cheat. Later, when you rescue him, Snake mentions Tatyana as his lover. Sokolov corrects him by saying that she's Volgin's lover. He shows a picture of his wife and says that "this is my lover." D'aww.
After killing The Boss, there is a hidden first-person view in which the player can see the ghosts of The Sorrow and The Boss, standing beside each other before fading away - they've been reunited in death.
Towards the end of the Snake Eraser short, Raiden is extremely close to killing Naked Snake and becoming the main character in the series (after a particularly painful Humiliation Conga), when he is nearly run over by the Shagohod. However, Naked Snake shoots the tank in time, helps Raiden get back up, and hands him a revolver. Raiden realizes that this is the perfect opportunity to kill Solid Snake's genetic father... But he can't go through with it out of respect for the man. Even though none of this is canon, there's something noble about it.
In the aftermath of the explosion at the Shagohod hangar, while the guards are fleeing for their lives, one can be seen helping another to his feet and carrying him away, shouting "Don't give up! Keep moving!" It's a nice little moment of humanity for the Mooks.
The culmination of Ocelot and Snake's final duel, from the former asking the latter's real name (and vowing not to forget it) to (if you picked the wrong gun) revealing that the special bullet he was menacing you with the whole time had been a blank, and cheerfully remarking that it had been good fun. Afterwards, Ocelot bails out of the plane without trying to carry the fight further.
If you pick the right gun, you can choose not to fire. When Ocelot wonders why in the following cutscene, Snake just smirks.
During one codec call Sigint reveals to Snake that he has had trouble finding work due to racism. But the Major doesn't care that he's black and hires him anyway. This is pretty touching considering that the series is set in the 60s. Plus it shows that the Major and Sigint are close.