Charlie attempting to help fix things between Paton and Miss Ingledew after Paton tells him about the disastrous date. Though his attempt ends in failure, it's heartwarming to see how much Charlie wants Paton to be happy.
Charlie's love and concern for his mother. At one point he worries that she is too remote and quiet.
The final line of the novel:
"It took Charlie several minutes to realize that the whole room was looking at him. His thoughts had been far away with someone else who had fallen asleep at twelve o'clock."
Charlie Bone and the Time Twister
Mr Pilgrim offering Henry oatcakes and giving him his cloak to wear after seeing that he's cold. He later also shows concern that Henry was left up in the Music Tower at all, as it's freezing at night up there.
Charlie offering to have detention with Olivia after Olivia gets detention because of something Charlie asked her to do, after realising that Olivia would be alone during the weekend. It's really sweet to see that he cares enough about his friends that he'd put his own problems on hold for them like that. Then straight after that there's Olivia insisting that Charlie help Henry and not worry about her.
Henry and James' reunion.
Charlie Bone and the Hidden King
In a round-about way, how Lyell begins to fade when Amy starts forgetting him in Charlie Bone and the Hidden King. It's kind of heartwarming to think that it's largely Amy who was keeping him alive for all those years by just remembering him. It shows how deep their bond is, that his life is tied to her memories of him.
Paton reassuring Charlie that his father won't fade away and isn't forgotten, because Lyell was a good friend to so many people.
Paton's outrage at hearing that Maisie will be transferred, and his making it clear that anyone who touches a hair on Maisie's head will answer to him.
Bartholomew Bloor's telling Charlie of his friendship with Lyell. He says that Lyell became the son he never had. And also his reason for helping Charlie defeat Harken: that he'd do anything for Charlie's father.
Amy and Lyell's reunion at the end of the book. Also doubles as a tear-jerker.
Charlie Bone and the Wilderness Wolf
Charlie defending his father when Lucretia insults him near the end of the novel:
Charlie: My father's worth a hundred Yewbeams!
It's particularly heartwarming since it's only been a few weeks at most since Lyell's been awakened, and already Charlie shows so much loyalty toward him.
Charlie Bone and the Red Knight
Charlie telling Cook that he'll never believe that his father didn't care about him or the city, and that he had to have a good reason for going away.
Lyell offering to adopt Billy at the end of the last book.
What makes it even more heartwarming is the knowledge that Billy is his best friend's son.
Henry and the Guardians of the Lost
Henry reassuring Ankaret during their trip back to Ocean View, when Ankaret is terrified that the carriage will turn back because of her.
Henry: Wherever we go we'll be together, and I'll make sure you come home with me.
Even though ten years have passed, Amy still wears the wedding ring Lyell gave her on her finger.
Paton's love for Miss Ingledew. He would do almost anything for her.