Fridge Brilliance: What happens to Amy and Lyell in the series shows the connection they have with each other. When Lyell is hypnotised, Amy becomes timid and a shadow of herself, and even Charlie comments that it is as if the spell that took Lyell has captured her as well. Both Amy and Lyell are trapped, Amy in her life in Filbert Street and Lyell in Bloor's Academy. After Lyell is awakened Amy becomes much more lively and self-assured and even plays a part in defeating the Bloors and Harken.
Fridge Horror: Mr Pilgrim's absence in the fourth book borders on this when you realise that he was being held captive in Yewbeam Castle the entire time while Yorath 'borrowed' some of his personality to be able to pass as a teacher at Bloor's. It gets worse when you consider what Paton went through in the third book when he went to Yewbeam Castle to stop Yolanda from coming to the city. Paton implies that Yorath 'borrowed' from him, and also implies that it was a tortuous experience. When you think of what Mr Pilgrim went through now, it's enough to make anyone scream.
Fridge Logic: Why was Mr Pilgrim unable to resist Manfred's hypnotic power in Charlie Bone and the Blue Boa? Because he'd already been hypnotised and didn't have any will left.
Amy and Lyell, after Lyell's awakening at the end of the fifth book.
Tancred and Emma could count as well, as at the end of the final book they do seem to have acknowledged their feelings for one another and are pursuing a relationship of some sort.
Ship Tease: Emma/Charlie in the third book, until Emma's found to have a crush on Tancred. Also Charlie/Olivia.
The Untwist: Seriously, is there anyone who didn't guess that Mr. Pilgrim was Charlie's father?
The Woobie: Billy Raven has this hard. Each book introduces some new torment that the poor kid has to go through.
Lyell could also count, in a way, but more in backstory than in the actual series. His father died when he was a baby, and his mother was a complete Jerk Ass who probably neglected him emotionally once she realised he wasn't endowed in the way she wanted him to be. He spent a good part of his childhood surrounded by nasty, cold-hearted relatives such as Yolanda and the Aunts, and judging from how terrible a sitter Aunt Eustacia was, one can guess how he was treated. On top of all that, his mother held a grudge against him because of a will and a letter his father wrote to him. He falls in love and wishes to marry, but the Yewbeams don't approve and forbid it. He elopes anyway, earning the ire of the entire Yewbeam family. Then, after just four years married and with a two-year-old kid, he gets hypnotised for life when he tries to stop the abduction of Emma Tolly and spends the next ten years in a deep trance, unable to remember anything about his old life. In the fifth book, when he's close to awakening, he almost dies because Harken bewitches Amy into forgetting him, and all because the Bloors and Titania don't want him to wake up and remember where he put the box that contains Maybelle's will. Even after his awakening, Lyell is still not completely himself again, with parts of his memory still missing.