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Tear Jerker: Goosebumps
The ending of The Ghost Next Door (both the book and the TV episode). The protagonist, after discovering that she was in fact the ghost that the title is referring to and has been dead all along, saves another kid from dying in a fire like she did. Then she rejoins her family in the afterlife.
The Haunted School, especially if you're familar with the Columbine/Sandy Hook shootings. The real kicker is the ending, where Thalia, one of the children who escaped Greyworld, chooses to return there so the protagonist can escape. Then, it's revealed the evil photographer from long ago is still alive, and ready to repeat his crime.
In My Hairiest Adventure, Larry's town is full of stray dogs that are left over from previous dog-to-children experiments. After Lily becomes a dog, her parents abandon their former daughter with the others and pretend she never existed. After Larry transforms, his parents, feeling remorse, stay behind to take care of him. This means that out of all the parents in town, they were the only ones who truly loved their assigned "child."
The scene in Deep Trouble where Billy and his family are being left to drown. The Comic Adaptation has an extra panel where he realizes how hopeless the situation is.
Carly Beth in The Haunted Mask is one of the biggest Straw Loser characters in the earlier books due to how she is constantly teased for being easily frightened. When Jerkass Steve plays a trick on her by getting her to eat sandwich with worms in it, everyone in the lunchroom laughs at her, including her supposed best friend Sabrina. In the TV show adaption, when Carly Beth returns home and finds that her mother made her a duck costume for Halloween, her brother uses it to scare her again. When she's alone, she just starts sobbing and rips the costume to shreds from how tired she is of being mocked. Thankfully, after her horrific ordeal with the Haunted Mask, she becomes much more braver and manages to handle Steve and his friends on her own.
If you think about it, the backstory of the masks. They weren't just demonic or evil, they were sentient creatures that were locked away because of their deformities and grew more and more twisted from the isolation. In the TV adaptation, we even hear them begging Carly Beth to be their friend as they chase her...
In The Curse of Camp Cold Lake, the ghost stalking Sarah is a lonely little girl who wants a friend to take to the afterlife. She had previously tried to do the same to Brianna, another camper, but Brianna's ghost refused to go with her. When you think about it, her being rejected a second time in years is heartbreaking.
In A Night in Terror Tower, Morgred the sorceror makes an emotional confession that he failed his king when he promised to protect the king's children, Edward and Susannah of York, from execution by their usurperous uncle. The High Executioner caught him before he could rescue them. Especially in the TV adaptation, where he nearly breaks down in tears when he tells them the truth.
The big plot twist of Ghost Beach. The kids that the two main characters met their first day are ghosts, 300-year-old Pilgrim children that died the first winter in the New World.
A more subtle one in The Cuckoo Clock of Doom: Michael is pretty obviously The Unfavorite to his Annoying Younger Sibling, and nothing he does is ever good enough for his parents, especially his father. Worse, as he goes back in time, the reader can see that it's been like this his whole life. As a twelve-year-old? His little sister torments him and his parents don't do jack shit about it, even calling him a liar when he tries to tell them. As a kindergartner? He ties his shoes for the first time (as he's mentally twelve it's easy, but apparently he'd been having trouble at that age) and all his dad says is, "Took him long enough." Even as a baby, at a stage where you can't really expect much of a kid, his dad complains that he's "slow" because his friend's kid is learning how to talk faster than his. Good thing the Twist Ending is happy for once - his sister is Ret Gone from existence and he is treated much better by both parents.
The Werewolf of Fever Swamp: Grady's dad preparing to put down Wolf after he's suspected of the Fever Swamp murders.
As cheesy as it may seem now, the TV adaptation has two particularly sad revelations: The Swamp Hermit was trying to hunt down the monster that killed his family. He dies trying to save Grady. Later, the werewolf partially changes back, revealing it to be Grady's friend Will, who is distraught by his transformation and warns Grady to stay away. Grady tries to find help for him, but Will realizes it's too late and dies after becoming a monster again.