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 extremly 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.
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.