The opening cutscene, before everything goes to hell, showing the Marston family actually acting like a family, something that was sorely lacking in the main game. Stuff like Jack and Abigail teasing each other, or Jack starting to ramble about Aztec mythology while John watches, clearly proud of how intelligent his son is. Even after Jack and Abigail get zombified, it's strangely touching to see John still trying to take care of them even when they're unintelligible and trying to eat him.
One of the random quotes John says when looting a dead body is something like "Jack, Abigail, the things I do for you." It really goes to show just how far John is willing to go if it might save his family.
Weirdly enough, a lot of the scenes involving Seth could be seen as heartwarming. The game's universe was already sucky before the zombie apocalypse, and Seth was no exception. He was an outcast who basically had his dream of finding a treasure crushed. It's strangely nice to see that even if the world is on the fast track to hell that at least one person's life was very much improved by it.