This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Children of the Red King
Midnight for Charlie Bone
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.
Charlie Bone and the Hidden King
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.
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.
Charlie Bone and the Wilderness Wolf
The murder of Asa's father in Wilderness Wolf. He and his wife trying to lead fear-crazed hunters away from their son, and in the process, he was mistaken for the monster they were hunting, and shot and killed. There's also the fact that he doesn't even get a proper burial - his injured wife has to bury him in a shallow grave pretty much right where he was killed, all the while knowing that if the hunters come back, she will probably be next. And that's not even mentioning Asa's implied feelings of guilt over the whole matter...
What got them into the mess is pretty bad, too. Asa changed sides to help Charlie save his father at the end of Hidden King, and was imprisoned underground by the Bloors for it in total darkness. Without light, he couldn't stay in his human form and would howl incessantly, causing humans in the city to start their hunt. His parents were simply trying to save him, and paid for it dearly.
Charlie Bone and the Shadow of Badlock
Tancred's drowning in Shadow of Badlock, and his friends' grief over it. One of the most cheerful, if sometimes pessimistic characters, dies Not to mention that he is one of the strongest characters in the series. Fans went nuts.
Charlie Bone and the Red Knight
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.
Charlie's loss of faith in his father over the course of the story. Particularly Charlie near the end saying, "Why did he go when we needed him?" Not even Paton has anything to say to that. It even goes as far as Charlie beginning to think that his father had run away and wasn't strong enough to stand up to the Bloors anymore. His feelings of betrayal, disappointment and doubt toward Lyell in this book is heart-wrenching to see, especially since Charlie had expressed such loyalty for Lyell when Lyell was still lost.
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.
Chronicles of the Red King
The Secret Kingdom
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 Stones of Ravenglass
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.