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.
The Executioner himself. He's a ruthless killer who will stop at nothing to find his targets, even if he has to travel through time to do so. Basically, he's a medieval version of The Terminator. Even the local wizard is terrified of him!
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...
On that note, another horrifying part is why she did and why she thinks the children deserve it: they bumped into her, causing her to drop her groceries, and didn't apologize. She puts two frightened children through a slow Transformation Trauma because they didn't say "sorry." And then in the ending, she does it all over again because they don't excuse themselves after burping.Disproportionate Retribution doesn't even begin to cover it.
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.
And there is also the Halloween party he goes to, where at one point is forced to bob for apples in a tub filled with living cockroaches, and has to eat one in order to stop playing.
In "The Haunted Mask", Carly Beth just wants a scary mask to teach her bullies a lesson that scaring people isn't cool. The mask she chose unfortunately is no ordinary mask and the mask becomes her face. She panics as she realizes she can't take it off and her friend advises her there is no line, no separation between mask and skin. That face becomes "her flesh"
Revenge Of The Living Dummy has a scene where Slappy sneaks up on the protagonist and pushes her down the stairs. Actually it was her cousin Ethan, who did so for the purpose of a prank. Could've killed his own cousin...for a prank.
In Creep From The Deep, the rotting forms of the zombie pirates are described in great, gory detail.
The plot of the story is kicked off when the protagonists' grandmother sends them to stay with their uncle, she's growing old, tired and weak. And when they get their, it turns out their uncle never picked them up, and they've been abducted by a complete stranger.
Ghost Camp is one of the most distressing and legitimately terrifying of the original books for a few good reasons.
Some of the pranks the campers pull included extreme bodily harm. One camper stabs himself in the neck with a fork and another has his foot impaled to the ground with a tent spike. Another extreme "joke" was Alex seeing an apparently dead girl floating at the bottom of the lake and trying to save her. The moment he got her to shore she just spit water in his face and said she could hold her breath for a long time. Of course, Alex learns he was right. She was dead.
Everyone at Camp Spirit Moon besides Harry and Alex are ghosts, but even they don't know how or why they died. All Lucy said was that the fog rolled in one night when everyone was at the campfire, and when it departed, they were all dead. We're never given a reason as to why it happened or how the fog killed them, it just did.
Also, literally the fact that Harry and Alex are the only characters in this book who aren't dead.
Lucy and the others have no idea how long any of them have been dead, and are unable to leave the camp or it's said they'll disappear and become part of the fog. How did they come to gain this information? How many people tried to leave the camp? Does that mean the fog is made up of lost souls stuck in perpetual torment?
Elvis possessing Alex at the end, and we're never told if he ever left Alex's body or if he's still inside him. And imagine what that must mean for Harry, since it's likely no one will believe his brother is being controlled by a dead kid.
Broken Dolls was another story that ran on the Nothing Is Scarier trope. We know the old woman did something to Tamara's brother, but we aren't told directly if she was trying to turn him into a doll or is she was stealing his soul to give one of her dolls perfect features. We're also given the implication that this woman has been alive for an impossibly long time, and there's an entirely unsettling moment made of Adult Fear during her confrontation with Tamara:
Dollmaker: Young people disappear so often in this century. You'll just be one more...
Then there are the implications regarding the old woman's dolls. At one point Tamara can hear them saying "Stop her" and they make motions as if they were reaching out to Tamara. The fact that Tamara heard cheers of happiness after defeating the old woman implies that the dolls were actually begging Tamara for help.
The Chalk Closet had a ridiculous title sure, but then comes the moment where Travis realized he did poorly on the exam and was going to be the sent to the aforementioned room by Mr. Grimsley. The scary part comes from the fact that Travis's classmates are all equally scared for him, but they're even more scared that they might get sent in as well, so they act as if nothing is happening, even as Travis is pleading for help.