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Nightmare Fuel: Goosebumps
I Live In Your Basement has a "girl" both turn inside out (in full detail) and has the main protagonist Marco cave in Keith's skull in with a paper weight.
The boy, Keith, also elicits very strange and disturbing stalker vibes, especially considering how young the protagonist is. Then there's the fact that the show descends into a complete Mind Screw after Marco gets hit in the head with a baseball. While it can be interpreted as Marco suffering from his concussion, the end actually reveals that Keith was having a nightmare about being a human and living above the basement.
The Haunted School, especially the sequence where the protagonist and his friend, who are in the black and white world that the missing kids from 1947 are trapped in, go outside of the school and are captured by savage kids who perform strange rituals for turning kids from the color world gray involving a vat of boiling oil.
The Curse of the Mummy's Tomb, in which anyone that violates said mummy's tomb is punished by being mummified alive!
Let's Get Invisible! has a mirror that can turn people invisible, but if you stay invisible too long, your reflection switches places with you while you get trapped in the mirror for eternity.
The Horror at Camp Jellyjam has a scene where one of the captured children tells the protagonist that if anyone stops to rest even for a second, that disgusting monster they're washing will pick them up and eat them. And that she's seen him eat three kids already!
A Night In Terror Tower is one of the creepiest and most disturbing books in the series. Two siblings are locked in a London torture chamber and are then chased by a menacing man in black. Then, when they get back to the hotel, they discover that they have no modern currency and suddenly begin to lose their memories, even of their parents and last names. It turns out that they are actually a prince and a princess from the Middle Ages (mentioned by their tour guide earlier in the book) who were sent forward in time and given false memories for their own protection, and the man chasing them is a notorious executioner who wants their heads on a platter.
One of the "rides" in One Day at HorrorLand involves the characters being sealed in floating coffins, which fill with insects.
In Chicken Chicken the protagonist Crystal (and her brother) are both transformed into chickens agonisingly slowly over several weeks in graphic detail. These included lovely paragraphs describing their eyes move to the side of their heads, their teeth sink into their gums, their fingers become bony claws and talons. Also Crystal grows a real beak at her best friends party and just asks for chap stick.
Vanessa herself. The mere thought of doing something like this to children and claiming they deserve it is appalling and sick beyond belief. And even worse, the story implies they weren't her first victims...
At several points in the book, a rumor is mentioned about a trouble making kid who got his head mutated into a sponge by Vanessa. Troy Steele thought of this as an annoying gag. However, considering what Vanessa did toCrystal and Cole, it probably wasn't just that...
In Even More Tales to Give You Goosebumps there is a short story called "The Perfect School" where troublesome kids are sent to a reform school. Turns out the school kidnaps the students and replaces them with "perfect" robots to send back to the parents. The Stepford Wives,anyone? The protagonist succeeds in going back home. Oh sure, he managed to not get captured and replaced by a robot, but his parents expect a perfect robot, so now he has to spend the rest of his life — or until he can move out — being absolutely perfect, for fear he'll get found out and sent back...
In the TV show it's a bit better, because his parents weren't expecting a robot so he can act at least decent and he's trying to break the other kids out.
Welcome to Dead House is very scary. Just the idea that a whole town could be out to get you, for something that is not your fault...
At one point Amanda describes a dream she had where her entire family were rotting skeletons eating a dinner of bones while her old best friend is trying to come into her house, but all Amanda can do is sit and consume bones with her dead family.
The whole plot. A botanist is doing strange experiments in his basement, and wants to keep out his kids. However, he starts to act strangely, growing more and more distant. Than the kids discover that their father is turning into some kind of plant creature that bleeds chlorophyll and has leaves in place of hair. And later they see that his plants have grown human features, like writhing arms and screaming faces.
In Headless Halloween, Brandon discovering his own corpse at the bottom of Raven's Ravine.