Nick's letter to Olivia after he was sent to jail. Olivia's three sentence response is equally heartwarming: That she believes him and she'll wait for him.
Gets more heartwarming, after the final events. If the player goes and talks to Olivia, she already sounds much happier compared to before. She even says that, after the events their marriage has been through lately and how they managed it, their marriage can withstand anything. It certainly took a heavy obstacle, but it has strengthened their marriage and made both of them much happier.
Keith, in general, is a sweetheart to diabetes-inducing levels. He's a dopey Man Child obsessed with rock 'n' roll and who vocally hates green peppers... Who also loves his wifeand children more than anything in the world, puts them before everything else in his life (yes, even his precious guitar), and who has no trouble at all treating the bizarre York like they're the oldest of friends. His sheer niceness is remarkably refreshing.
The entire ending for the Director's Cut. From the reveal of Zach having a family and living happily throughout his life, to finally being reunited with York and the Goddesses.
Despite everyone's wariness, York is surprisingly gentle and considerate when he questions the Ingram boys - one of the first signs that there is a softer side to him. Of course, it makes sense that he's decent with kids, given that York's been guarding a traumatized boy's psyche for the past couple decades.
Harry telling Michael, his adopted son, that he's proud of him.
York's relationship with Zach, while incredibly vague, is very sweet. Whenever he speaks to him, there is a gentleness in his voice that is never shown when he speaks with any other character, and it's clear throughout the game that whoever (or whatever) Zach is, York genuinely cares about him. In the climax of the game, he even sacrifices himself so that Zach can finally regain his own body after years of being locked away in the Red Room.
During Becky's death, there's a very heartwarming moment of Anna, in her Goddess of the Forest dress, reaching out to Becky with a smile on her face. It's especially touching since Becky's diary revealed that she ran away when Anna was being attacked, and couldn't forgive herself. Yet Anna's spirit reached out in kindness. Later, when Becky went to visit The Tree of Anna Anna let go of the locket, the clue to catch the killer, so that Becky could secret it away to Diane.