When you talk to Sandy "Moose" Jansen in the back corner of the police station turned into a makeshift survivors' fortress, you get some back story on the past couple events from his point of view. You learn that he was originally one of the people in a trance like state walking towards the mysterious sea fog until Deputy Andy finds him, ties a rope around them both, and acts like an anchor until it's over thus saving Moose's life. Moose makes it apparent that he is perfectly capable of leaving the cursed town and surviving on his own but refuses to leave Andy who refuses to leave the town and its surviving people. It's both heartwarming and heartbreaking when he basically tells you that he's in an unrequited love with the Deputy who may only ever see him as a good friend.
The intro of "To Sir With Love." Upon learning that there's a wraith haunting Innsmouth Academy as a result of his early magical experiments, Headmaster Montag decides to kill himself in order to banish it... whereupon Usher and Carter immediately refuse him. Usher and Montag's professional relationship might be eccentric at best, and Carter doesn't have any reason to see him as anything other than a creepy teacher with a habit of giving nightmarish lectures, but they're not ready to let him die- even if it's for a good cause.
Unusually for Montag, he actually manages to seem proud of Carter when she admits to knowing the exact details of the sacrifice he's about to perform.
A small one, but in Savage Coast, in addition to John Wolf's...wolf, there's a dachshund sleeping in a basket beside him.
The Ugly Cute nature of some of the vanity pets can make them extremely endearing, moreso than the normal ones. We're pretty desensitized to adorable cats these days, but replace "cat" with "cat-sized undead moth" or "dog-sized squishy blobby big-headed tentacle thing that jumps up and down," and you get some really weird d'awww moments.
In Blue Mountain, Eleanor Franklin appears to be curiously uninformed and untouched by recent events. When speaking with her about the Fog it is implied that her deceased husband Ed saved her life by keeping her inside the house. In a game where the ghosts are largely angry or malevolent, it is a testament to the love Ed still holds for his wife that he actively tries to protect her.
Harumi and Yuichi's entire relationship.
During your initial meeting with Jung, he gets a bit upset about being the only one of the children left in the playground after the hell Orochi put him through. Your character, in an extremely sweet gesture, proceeds to help start up his solitary seesaw.
While wandering through the floors of Orochi Tower, in addition to the expected experiments gone wrong you also find things like thank you messages from recipients of artificial limbs and organs made by the Orochi Group. Despite having a graveyard of skeletons in their closet, the Orochi Group has helped humankind as well.
When the two little Roma children, Tibor and Luminita, are discussing their respective mentors Mihas and Zaha, Tibor remarks that he things Mihas likes Zaha, and Luminita responds that he's out of luck because Zaha's a lesbian. The unconcerned, matter-of-fact way she says it makes it clear that it's not a big deal, which is incredibly heartwarming if you know how conservative and often homophobic eastern European culture can be.