Just after meeting the ninja, Berthold is severely electrocuted and almost dies. Sniper Wolf petting him when he regains consciousness is just the sweetest thing.
Sniper Wolf giving Liquid the dog tags of his "father" after he regained his body.
Coming from the two most otherwise despicable members of the group, Ocelot and Mantis' genuine offer of companionship to The Sorrow and offer of their library is surprisingly heartwarming, especially Ocelot point that Sorrow is no weirder than any of the others and could belong with them. It's particularly interesting for the offer to come from Ocelot, as The Sorrow is a being he has no possible means of controlling (and who could have easily known things that might have been detrimental to his plans), and for Mantis - who would usually rather kill people than connect with them - to jump in to help convince him.