Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: Goosebumps
I Live In Your Basement has a "girl" both turn inside out (in full detail) and has the main protagonist 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. The Mind Screw does not help at all.
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 cover deserves a mention. At first, it looks like a normal open locker with a bunch of papers falling out of it, with the inside pitch black. But if you look closer, there are eyes staring out at you.
The Curse of the Mummy's Tomb, in which anyone that violates said mummy's tomb is punished by being mummified alive!
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!
And by extension, what happened to those kids that the monster ate after Wendy suffocated him?
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 pair of historical figures 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. From Bad to Worse, indeed.
One of the "rides" in One Day at HorrorLand involves the characters being sealed in floating coffins, which fill with insects.
The scary ending of the Tales To Give You Goosebumps story "Click", where, as a consequence of his selfish actions with the remote which can control the real world, Seth is left in a dark void when the remote runs out of batteries, leaving the real world a barren wasteland of emptiness.
Welcome To Camp Nightmare's head monster.
Ghost Camp has some surprisingly gory descriptions for the series. Including severed heads, poles through feet, people stabbing themselves in the neck with forks, and dead bodies in water.
The dream sequence in The Scarecrow Walks at Midnight where the scarecrow is tapping on the kid's window and then he runs out to see her grandparents as scarecrows too.
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 being absolutely perfect, for fear he'll get found out and sent back...
In the TV show it's a bit better, because his parent's weren't expecting a robot so he can act at least decent and he's trying to break the other kids out.
The TV adaptation of Night of the Living Dummy. For one thing, at the climax, Slappy's in the air vent, they're going to the front door—oh God how did he get out?!—and so they run down to the basement to get out the window andHOLYCRAPHEGOTOUTSIDE. But it's the ending that makes it creepy.
Night of the Living Dummy III had an attic full of dummies.
My Best Friend is Invisible from the TV show, when the parents reveal their true faces. Those faces, while badly imprinted, are quite horrible.
In Be Careful What You Wish For, a bullied girl named Samantha Byrd has three wishes, each of her them getting warped in a different, unsettling way (for the record, each is cancelled when she makes the next one. The first one makes her the best player on her basketball team - by making everyone else deathly sick and unable to move. The second has her wishing Judith would "go away", and everyone else in the world, barring Samantha and the fortune teller witch, vanishes from existence (in the tv episode, she wishes everyone would "buzz off", resulting in everyone in the world turning into flies. Her third wish is that Judith thinks she's the greatest person to ever live. It works... A littletoo well. At the end of the story, because of her dissatisfaction, she's given an extra wish as compensation and her last wish is that the bully Judith had met the witch and gotten the for instead of her - the first thing Judith says to Samantha is "Why don't you fly away, Byrd?", and Samantha walks off and ends up as a bird. The idea of remaining a bird for the rest of her life is rather unsettling, but in the TV episode, it becomes worse - with her set of wishes, Judith's first 'wish' is that everyone would admire her. She is turned into a statue.
What's even creepier is that the witch, Clarissa, offered Samantha these wishes in the first place because she appreciated Samantha helping her out, and claims that the wishes work out that way because she can't control the exact outcome. Whether she's lying and is really a cruel sadist or she's utterly sincere but can't help ruining the poor girl's life due to imprecise magical ability, it's very disturbing either way. Though Samantha seemed to be happy as a bird, which despite being a transformation-induced state is at least a more carefree way of living than she previously had...
That last part is still nightmare fuel in a fridge horrory sort of way; How badly must Samantha's normal life suck to make her think that being permanently transformed into a bird is a good thing?
In Bad Hare Day, a boy named Tim becomes wrapped up in a scheme with a creepy, sleazy magician, Amaz-O. The book ending reveals that Amaz-O was a life-sized marionette operated by a rabbit who used to be Amaz-O the magician (who got turned into a rabbit by a real magician) and makes a deal with Tim to become a rabbit so Amaz-O can presumably go back to being human. At the end of the TV episode, both the boy and the magician are turned into rabbits due to a spell accidentally cast by the boy's little sister. It is implied that they will remain rabbits for a long time...
Not that Tim seem to mind (at least not in the TV episode).
Amaz-O: Don't worry, Tim. I'll figure out a way to get us out of this. Tim: What? And give up show biz?
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...
In Headless Halloween, Brandon discovering his own corpse at the bottom of Raven's Ravine.