Emilia's grief when she finally wakes from her trance, and her broken words: 'I didn't think I was so unhappy. All my life I've lived with people who didn't love me.' In fact, the entire scene is a huge tearjerker, as you see Emilia weeping and rocking and Charlie, Olivia, Benjamin and Fidelio watching her helplessly.
When Amy and Charlie go to bring Lyell home in Charlie Bone and the Hidden King, they see Lyell in the academy's chapel and Lyell doesn't recognise them. Amy's reaction to seeing Lyell alive and her despairing cry only adds to the emotion.
Tancred's drowning in Shadow of Badlock, and his friends' grief over it.
My Greatest Failure: Paton Yewbeam never really forgave himself for not helping Lyell at the cathedral on the day he disappeared.
In the first book, Paton goes into this after his disastrous date with Miss Ingledew.
Paton also goes through this in the third book when Ms Ingledew is dying from wearing a bewitched belt. The look on his face when he realises he can't save her is heart-wrenching. luckily Charlie and his wand are able to revive Ms Ingledew.
There is also another one in the same book when Paton is ill from whatever Yorath did to him in Yewbeam Castle.
Amy seems to go through this for a moment at the end of 'Hidden King', after Manfred smashes the bottle of King's tears onto the floor to stop Charlie from awakening his father.
Heroic Sacrifice: At the end of Charlie Bone and the Castle of Mirrors, Billy Raven's guardian Christopher Crowquill sacrifices his life to save Paton's when Yorath Yewbeam tries to kill him, because he's dying anyway and Paton is the only one who can protect Billy.
The entire scene where Charlie is using the Mirror of Amoret to discover where his father is. After remembering (with Claerwen's help) a memory of Lyell smiling and playing the piano in Diamond Corner, the Mirror takes Charlie mentally to the Music Tower, where Lyell sits slumped over the piano and looks half-dead. And when Charlie calls out to him, he tells him to go away and 'There's nothing left'. Charlie's reaction (a terrible scream) to seeing Lyell almost dead is particularly heartbreaking. It's saddening to see that the smiling man in Charlie's memory has become the dazed, almost dead man Charlie visits in the Music Tower.
The reality that Lyell never got to see Charlie grow up, and that he lost ten years of his life just because the Bloors decided he had to be punished for 'breaking the rules' and trying to prevent the abduction of Emma Tolly.
Every single scene where Charlie meets his father by chance in Bloor's Academy, when Lyell is still spellbound. It's hard not to cry when the reader sees Lyell trying but unable to remember, and Charlie talking to his father without knowing who he is.
Every single time Paton, Charlie and Amy think or speak of Lyell.
Charlie's pleasure when Cook says he is 'wise beyond his years', and the narration that no-one had ever called him that before, that in fact they said the opposite. Which means that he spent most of his childhood being called 'stupid' and 'foolish'. The only people who said otherwise and actually gave him love were his mother and Maisie. It's actually similar to Petrello's experience in Leopards' Gold, where Nurse Ogle and his mean older siblings call him 'Foolish Petrello', to the point where Petrello believes it and thinks he will never make anything of himself.
Also at the end of the eighth book, when Lyell tells Charlie that he (essentially) saved his life in the battle. Charlie's surprise at that is heart-wrenching.
In The Secret Kingdom, Timoken's grief over his sister's disappearance and possible death is made even more heart-wrenching when you remember that his parents were killed by viridees long ago, and Zobayda was all the family he had left. After Zobayda's gone he has no one (well, not counting Gabar the camel, that is). Timoken can't even mourn her properly according to the customs of his people, as he's being constantly chased by evil viridees and it would be dangerous for him to stay in the forest for too long.
Berenice's grief over her father's death in The Secret Kingdom. Upon hearing the news she faints and breaks into sobs and moans. Then she gets back up and swears vengeance on his murderer.
The tears on Eri's face when he admits that the baby that Beri brought with her to the Red Castle in The Stones of Ravenglass is his grandson who was orphaned when the conqueror's men murdered Eri's son and daughter-in-law.