Much of Animorphs is a deconstruction of Wake Up, Go to School, Save the World, and it's one of the clearest and most prevalent examples of War Is Hell in children's literature. By the start of the last book, The Beginning, they've spent three years fighting a horrific war, just trying to Hold the Line until the Andalites show up and bring enough of a fighting force to stop the Yeerks. None of the main characters are in anything even close to a healthy mental or emotional state. One of them sent his cousin to kill his brother, knowing she'd die too. And she agrees with his decision because she doesn't think she'd be able to function in normal life without the war anymore. Another spearheaded a plot to kill his own mother because she was the host for one of the Yeerks' leaders. A third was trapped in a body—and a species—not his own in the first book. It's much darker than its market would suggest.
Lemony Snicket's A Series of Unfortunate Events. A story about a man who murders just about every character in the series trying to kill three orphans to get their inheritance. This includes characters being eaten alive, death by harpoon gun, and the untold unmentionables who didn't escape the hospital fire. Completely justified, since it comes with the Snicket Warning Label.
Coraline. Full of distinctly Freudian terror, but the true creepiness of the book isn't always apparent to kids, who might see it as just a book about scary monsters.
Darkest Powers series is essentially the same as its dark, adult oriented The Otherworld sister series but aimed at a younger audience. It's somewhat more toned down. Basically only the sex and profanity are taken out. Thus we have a series about teenagers trying to escape getting killed and one of them doesn't with plenty of Body Horror and Nightmare Fuel sprinkled about.
The Demonata, also by the real Darren Shan, is another ultra-violent horror series involving demons. And just like the Saga, it's meant for kids. Among the not-so-kid-friendly elements:
Said uncle's sexy best friend also, at one point "accidentally" spills milk all over her shirt, and calls the narrator in to help her out of it.
And, by book five, it all starts to go downhill.
Department 19: With all the grisly violence and gore, you'd expect the novel was for adults.
While Robin Jarvis' Deptford Mice books feature cute animals, their being targeted at children is very questionable because many of the characters are subjected to violent, absolutely horrific deaths such as being skinned alive, decapitated, or having their body slowly eaten away by a deadly poison.
Most of the people getting up in arms over the blunt descriptions of puberty and other "naughty" things found in The Diary of Anne Frank are forgetting the fact that the book was written by, you know, a 13-year-old girl dealing with things every 13-year-old girl goes through (well, minus the whole Nazi thing). It was a personal diary after all.
The Amazing Maurice and His Educated Rodents is deep (the rats are inventing their own morality as they go), terrifying (the rats face vicious terriers, powerful traps and a Mind Controling villain), and squicky (the "inventing their own morality" includes the idea that maybe they shouldn't eat other rats, or at least not the wobbly green bit, but the eyes are fine).
The Tiffany Aching novels have a preteen (to start with) witch facing various inhuman creatures, including the Queen of The Fair Folk (one of Pterry's nastier villains) and a being of pure hatred towards witches. The next-to-last book begins with an abusive father beating his pregnant daughter into a miscarriage, and nearly being lynched by his disgusted neighbors. All the books also feature references to sex, which become steadily less coded as they go on. Interestingly, Wintersmith and I Shall Wear Midnight don't use the "smaller hardback" format of Maurice and the first two Tiffany books, although they're still listed as "for younger readers". Terry's view is that allDiscworld novels are aimed at anyone who understands the jokes.
Special mention to the constant Adult Fear of having lost your entire family but one, and having that one constantly in danger.
The Gone series by Michael Grant was made with teenagers in mind, but the books contain such extreme violence that a warning is actually required. Features such characters as a sadist with a whip hand, evil talking coyotes who want to end all human life, a girl who can make people see all sorts of unholy terrors, and so on. The fourth book contains people coughing up their organs, and bugs eating people from the inside out. The less said about the last book, the better. It's easy to see why there aren't movies of these books...
For those not familiar with his work, Neil Gaiman does not believe in talking down to kids. He has also reached the conclusion that children often enjoy horrific stories more than adults, which dovetails with his observation that, unlike adults, many children know no mercy when it comes to what happens to villains (cf. the deaths of many of the villains in beloved fairy tales).
The Girl Of Ink And Stars has a premise that sounds innocent enough: the Plucky Girl protagonist must journey into the forbidden forest and use her skills with map-making to find her Spoiled Sweet best friend. However, the story itself features said protagonist growing up in a town ruled with an iron fist by a cruel Governor (who whips people and does other horrible things) corrupt law enforcers, demon attacks, descriptions of the decaying environment, and, early on, the town being spooked by the brutal murder of a THIRTEEN YEAR OLD GIRL. It's also rife with Adult Fear, and features such lovely scenes as the search party finding a desolate village filled with bones and an 'X' made from dried blood and dog teeth.
The book also doesn't shy away with its descriptions of blood, wounds, scars, or how much Isabella's journey is wearing her down, physically AND mentally. It's not gory or anything, but it still gets quite dark at times.
The Grisha Trilogy has an in-universe example with the Istorii Sankt'ya, a book of religious stories for children which contains extremely graphic illustrations of saints being martyred.
Harry Potter has one of the best examples of this trope in the Deathly Hallowsfilm, which has a scene that caused major uproar (among Moral Guardians and parts of the fandom): Naked Harry and Hermione making out — a vision which Ron sees as the locket shows his worst nightmares. Another is Bellatrix writing on Hermione's arm with a knife. Sure, we all know that Cruciatus is worse, but it is perceived as unreal. When Umbridge forced Harry to carve words into the back of his hand, it was also done with a magic medium, and therefore less visceral.
Harry also grows into the world of moral ambiguity increasingly as the books progress and he ages, until a large part of the seventh reads more as a Deconstruction of the Kid Hero trope and associated character tropes than a straight fantasy climax. Especially the Dumbledore material.
The very nature of the one book = one school year ratio forces this. Even if there were no magical elements at all, 18-year-old graduating high school seniors face very different issues than 11-year-old sixth graders.
She's also had to point out to those that say the first book was much lighter than the others that it does open with a double homicide and the attempted murder of a defenseless infant, although quite frankly it opens with a boring man driving home from work, the attack in question having happened before the story began.
Her point still remains. The first book also contains: the strangulation of a child, head-bashing, gruesome injury and descriptions of blood, graphic descriptions of burning, and the death of a man, caused by an 11 year old boy who was just trying to defend himself from attack.
1997 children's adventure book Haunted Castle definitely fits this trope. Due in part to the amazing art of artist/writer Leo Hartas, complete child-friendly scenes such as demented, crumbling paper-mache clones of the protagonists, a man being crushed feet-first by a garden roller while still alive and swimming through the guts of a gigantic fish are all brought to your children's nightmares!
This is a large part of the reason why In the Night Kitchen by the late Maurice Sendak was banned from various school libraries and children's book shops: The child protagonist Mickey loses his pajamas for some reason and ends up naked for a substantial chunk of the story, with his nudity uncensored.
I Want My Hat Back sounds and looks like its aimed at a very young audience however the rabbit being eaten by the bear in revenge is certainly not something you see in most picture books.
Lauren Myracle's The TTYL Series have cute covers with 8-bit emoji, and they're about three girls who are friends and are in school, and communicate fully through instant messaging. What could possibly go wrong?! Everything: lots of swearing, plus mentions of anything sexual you can think of (like masturbation, oral sex, erections, fondling, porn, anything), and glorification of alcohol and drugs. Despite all this, they are marketed towards pre-teens, are sold near kids' books, and have no warnings on them whatsoever about the content inside. To make it even worse, Lauren Myracle has created books that are much less ambiguously for kids.
Mama Ga Obake Ni Natchatta, a Japanese picture book from Nobumi (who is also a character designer for NHK's Miitsuketa and Okaasan To Issho), is about a child and the ghost of his mother. While the book is intended for ages three and up, some parents complained that it is too emotional and scary for children.
Phenomena: While the main series is dark enough already it is with it's strangely 9+, Azur's spin-offs are said to be for younger children. The first 4 books are filled with suspense, he's banned from his home and he's kidnapped and tortured, in the 5th book his brother is seen covered in the blood of innocent people, in the 6th he, himself, is seen covered in blood of innocents eating of an uncensored torn off leg complete with a Slasher Smile, on the cover! Worse still, the books are illustrated so you can see his suffering on every page.
The Jolsah's spin-offs meant for the same age group, aren't much better, it even features a mad man that wants to cut things of Jolsah while alive and an evil man wearing an elf's scalp which the other guy cut off so if they do something bad the elves are blamed. It's not even an horror series!
The 1st book might be a Cliché Storm to some, and then the 2nd book◊ comes. There the Chosen Ones are drawn down into the sand by some beings eating everything! When Azur protects them and they are "free" to go, are the other terraqus'es mad at him, so they eat their OWN elder instead. When they are accending to the surface are they passing by some terraqus'es eating something, it's mentioned that it looks familiar and quite fresh looking although almost eaten up, and it's heavily implied that it's one of the children's ahmel...
Redwall. Cute furry creatures killing each other with swords, bows and arrows, spears, poison, and whatever else comes to 'paw'. Multiple instances of murder and torture, not all of it off-screen. Slavery, cruelty, major battles, and almost anyone can die.
Book two mentions marijuana (or some other herbal drug; it's not mentioned by name) and 'shrooms.
Book eight has a character who, though appearing to be fifteen (and probably around the same stage of puberty as any real teen), is really about 27, first outright saying that he wants to date said real teens ("That's the thing I love about high school girls: I keep getting older, they stay the same age") and then trying to do... something to his much-older teacher (who is very likely younger than him.)
Plus, the books are so violent and gory, it's not even funny.
Scary Stories to Tell in the Dark is best known for traumatizing a generation of children with its less than child-friendly illustrations◊. Suffice to say, it spent the better part of two decades holding the top spot in ALA's list of most challenged books, and was only knocked out of the top ten after the publisher caved and re-released it with less disturbing images.
Skulduggery Pleasant is marketed to preteens. It features the charming adventures of Skulduggery and his young apprentice Valkyrie who spend their time searching for clues and engaging in witty repartee and—Oh, Crap!, did the Grotesquery just rip off someone's head? And, um...Darquesse? This is a kids book. You can't go playing football with people's brains.
The Varjak Paw books are marketed for kids, but are full of inhuman viewpoints, death, mutilation, starvation, general creepiness, and the implication that the Big Bad is taking cats and turning them into walking, talking toys, or silent, deadly killing machines, somehow. Being illustrated by Dave McKean (as is Coraline, above) probably doesn't help much, either.
Wagstaffe the Wind-up Boy is a textbook example of What Do You Mean, It's for Kids?? The amount of anger and nihilism that permeates this supposedly funny story is notable; nowadays you'd call it Black Comedy. Everyone is unsympathetic. This book was not written by happy humans. Furthermore, some of the scenes... well... The main character is pancaked by getting run over by a truck. There's illustrations. Amazingly he's still alive when two workmen try to scrape him into a bin bag. Later, after he's been rushed to hospital and the renegade doctor's team turns him into the wind-up boy, they discuss what to do with the left-over organs. "It'd be a shame to waste them on the dog - he's so young and tender." They eat his heart and pancreas. "And very nice it was too", she tells Wagstaffe.
Watership Down. Despite what one may think of the movie, author Adams wrote the original book as a bedtime story for his daughters, and has always maintained it was for children. In one edition's foreword, he even talked about how happy it made him to see kids enjoying it.
The Wings of Fire series is normally a kid-friendly adventure series in a world of dragons, with a few bits of intenser-than-usual violence. (Which is to be expected, as the author was also part of the team that worked on Warriors.) However, some of the books feature surprisingly mature themes, especially the third and fifth books. The third book explores the character of Glory, who is a victim of an especially abusive childhood and deeply ingrained bigotry against her own kind, played very seriously. The fifth book, meanwhile, is all about Sunny, an often looked-down-uponcutie who then proceeds to discover Nietzchean nihilismafter her worldview is shattered. Also, special mention to Darkstalker, which features a character who has PTSD after watching his family be massacred and thinks about self-harm in one chapter another character having some utterly horrifying visions of the future, another character whose parents are in a seriously dysfunctional relationship, and an ending that involves one of the protagonist using a mind control spell to drag his own father out in public and make him cut his tongue out and then disembowel himself with his own claws.
Charlie and the Chocolate Factory: Perhaps kidlit's defining Black Comedy, as naughty children are subjected to a variety of dreadful consequences ranging from near-drowning to falling down a garbage chute that leads to an incinerator. While the novel has the kids survive, they're very much changed for their experiences, and adaptations have played with their fates — they're ambiguous in the 1971 film, and the 2013 stage musical goes with possible Death by Adaptation (if they're lucky, they'll get a Disney Death or rescue, but only offstage). Making matters worse, the factory proprietor has No Sympathy for them! This doesn't even get into adaptation-specific twists and references: the 1971 film has the notorious boat ride and the line "I am now telling the computer exactly what it can do with a bar of chocolate!". The 2013 musical has multiple jokes about alcohol and/or drinking problems amongst the adult characters.
The Witches: The very nature of the witches — a race of child-hating hags who live only to rid the world of them by any means neccessary, the crueler the better — is disturbing enough to put off sensitive adults.
The Underland Chronicles. Yeah, is still a book series aimed at older children, even though it contains a massive amount of extreme violence such as decapitation. Wounds are even sometimes described in explicit detail. Maybe the fact that it's written media and not shown as actual pictures keeps the Moral Guardians away.
The Hunger Games: The age recommendation for these books - 11, 12, 13 - is surprising to some parents, reviewers, and even older teen readers. Maybe it's the inclusion of decapitation, suicide, torture, mutilation, child prostitution; death by fire or venom, being buried alive, and other psychologically and emotionally disturbing content that raises their eyebrows, or maybe it's the fact that Katniss, the viewpoint character and protagonist, is sixteen and the book appears to focus on the fears and themes most relevant to that age group.
Descriptions of the author's next book are interesting too: Year of the Jungle — about her childhood during The Vietnam War — is picture book for four-year-olds.
Lots of works by Astrid Lindgren come off as really dark for being children's books, when you read them again as a grown-up.
Mio, my Mio is very much like the first couple of books in the "Harry Potter" saga. That is, it opens with a realistic portrayal of child neglect/abuse, but the protagonist then is taken to a magical world, where everything seems to be lovely and fun, only to realize that he has to fight a really creepy villain, whose very name is enough to scare people, and his equally creepy henchmen.
Sunnanäng was a collection of four short stories, which all push the boundaries for what parents will want to read to their children. In the first story, two little orphans are painfully neglected/abused. And in the second story, another orphan is forced to live in gruesome poverty among a bunch of elderly people (and she also has to give her soul up to make a tree able to play music. And in the third story, we get a pretty graphic description of sheep being killed by a wolf, and a girl gets abducted by the fair folks. And in the fourth story, a feverish boy (who is very close to dying) dreams about him being a knight in Medieval times, who has to sacrifice his life to save his king's life.
Emil i Lönneberga is mostly a light-hearted franchise, but the last book includes Emil saving a new-born piglet from being eaten by his mother, getting "drunk" when he eats fermented cherries and saving his best friend from dying from blood poisoning during a blizzard.
The Brothers Lionheart might still be the worst offender though. The protagonist (a nine-year-old boy) is sick from tubercolosis, but his beloved brother dies before him when he saves him from a fire. And when it seems like the brothers can be happy together in a magical land after death, they have to start fighting an evil dictator and a creepy dragon. (To be fair though, this book has reportedly been a great comfort for terminally sick children.)
Madicken can be rather dark too, especially in the second installment. The neighbor has to sell her body to science, so she can give her alcoholic husband money to pay off the mortgage. Then a girl is publically canned in front of her classmates in school (she had stolen the headmaster's wallet, but still). And a deranged man almost abducts both of Madicken's younger sisters, and we also have Madicken's crush almost dying from pneumonia.
Despite being fairly new to the kid's book scene, Brandon Mull is pretty good at this.
The Fablehaven series starts off very tame, like most other YA fiction, but when you get to, say, the extreme violence at the end of Book 2, the death-by-dissolving in Book 3, and Naverog's eventual fate (chomped in half, with his bleeding torso stump slumping to the ground), you start to wonder.
Pretty much any book by Garth Nix that's labeled as "young adult" (as in, the stuff usually found in the kid's section). For example, there's the series that has living (often unfriendly) shadows, Mind Rape as capital punishment (even for minors!), Body Horror, and some rather intense war scenes. Then there's the one with Mind Screw galore, Body Horror monsters, mandatory brainwashing (more literally than the word is usually used) for children, and plenty of death. Oh, and the ending involves the destruction of everything everywhere everywhen. For those of you asking how this can possibly be meant for children, go and read the Old Kingdom books. You know, his teen series.
John Bellairs wrote gothic horror novels intended for children full of all sorts of subtle Nightmare Fuel.
Anything written by Robert Cormier would count here, especially The Chocolate War and Fade (two books that frequently make it to "frequently banned books" lists) but not limited to those two books. His novels were specifically written for older children and preteens but are about anything from terminally ill children being used as live guinea pigs (The Bumblebee Flies Anyway) to a young boy with amnesia who's being marked for death as soon as he regains his memory (I Am the Cheese).