A truly heartwarming moment occurs when it is revealed that Merry, previously presented as Cain's illegitimate half-sister, is not actually biologically related to him at all. He took her in, loved her, made her his heir, and never revealed to her that he had evidence all along that she wasn't really a Hargreaves.
Also the fact that Uncle Neil knows about this, yet decides not to reveal it as he has come to care for her as well. Especially considering how he was previously not above using her adoption into the family as a bargaining chip when dealing with Cain. Neil's character development itself is rather touching, as it's slowly made clear that his brusqueness is just a coverup for how much he loves Cain, and that all his interferences in Cain's life are done in an effort to protect him.
Pretty much everything Riff ever does with regards to Cain when his kind personality is dominant, including that he somehow always knows how to find him. It seems to be ruined when evil-Riff explains that he had a "thunder stone" that vibrated when in proximity to Cain's earring, functioning as a tracker... then comes right back around to heartwarming when good-Riff manages to take over the body again and explains that he never needed to use it. He "reached out and listened to the air" and could tell when Cain needed him.
Cain embracing his Uncle after the Jack The Ripper fiasco. Both have difficulty showing their love for the other and Cain does a first step to try to be more open with Neil.
Uncle Neil telling Cain that he never protected Cain because he was Augusta's child, but simply because he began to love him when he was just a baby and reached out to him on a whim. The ensuing hug between the two is something that makes it all the better.