The Alex Rider series by Anthony Horowitz, so you think this is a fun for young teens novel series? not quite, the titular character is just a fourteen year old by manipulated to work for MI6, he then endures many horrific things over a single year. This series can be considered the Neon Genesis Evangelion of Spy Fiction.
They have a large amount of violence, horror, some swearing, and one use of the word "balls".
Animorphs features a lot more violence and horror than you would expect, despite being for kids.
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 L Abel.
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. It's somewhat toned down, basically just the sex and profanity taken out. Thus we have a series about teenagers trying to escape getting killed and one of them doesn't.
The Demonata, also by the real Darren Shan, is another ultraviolent 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.
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 12-year-old girl dealing with things every 12-year-old girl goes through (well, minus the whole Nazi thing).
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 pre-teen (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 last book begins with an abusive father beating his pregnant daughter into a miscarriage, and nearly being lynched by his disgusted neighbours. 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.
Mr. Hoppy, a Shrinking Violet who is in love with the woman below his balcony, Mrs. Silver, impresses her by buying many tortoises and using a mechanical gadget to take Mrs. Silver's tortoise Alfie up to his floor and send a larger tortoise down, to make it look like Alfie is growing bigger (Mrs. Silver was complaining that Alfie had only grown three ounces in the eleven years she had owned him). This impresses Mrs. Silver enough to give Mr. Hoppy the courage to ask her to marry him, and she accepts. In short, a man gets what he wants through lies and deception.
Mrs. Silver once tells Mr. Hoppy that if he can make Alfie grow bigger, she'll be his slave for life. This raises quite a few eyebrows.
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).
Harry Potter. The Harry Potter example is so prevalent that some editions of the books have plain covers in dingy earth-tones (as opposed to the colorful fantasy illustrations that the "main" editions have) so that adult readers don't have to feel so embarrassed when they read it on the train. Considering most children's books are written by adults, you think adults wouldn't feel they needed to justify reading a children's book in the first place... After all, if the author isn't embarrassed at having written, why should an adult feel embarrassed at reading it?
One of the best example of this trope is 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.
Though Rowling's The Casual Vacancy makes all her previous books look like fluffy bunnies, even the darker ones.
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 defenceless infant.
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!
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.
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.
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, alongside Unfortunate Implications: 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.
Phenomena: While the main series is dark enough already it is with it's strangely 9+, is Azur's spin-offs 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!
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.
Skulduggery Pleasant is marketed to pre-teens. 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, umm.... 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.
A lot of books by Astrid Lindgren. Including, but not limited to, children and beloved elderly people dying, Nightmare Fuel monsters, and very realistic and heartbreaking descriptions of the problems with alcoholism and poverty.
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.
The Choose Your Own Adventure books were sold to kids as offering the ability to play the title role in a kid's adventure book. They are, however, remembered for the terrifying endings that arise when incorrect choices are made, with some books even giving detailed descriptions of being eaten, shot, stabbed, poisoned, torn to bits, electrocuted, immured, trapped in tortuous time-loops forever, and so on. These older books are generally no longer considered suitable for children, although the creator of the series - Edward Packard - said in an interview in 1981 that in his experience children enjoyed the exaggerated deaths.
Fairy Tales were written for peasant children who grew up in rather a Crapsack World. What would be considered fit for them would be different then what is considered fit for modern suburban kids. Although it might be argued that even these generally have a stronger stomach then many adults realize. Some of them were originally written for adults. In these cases, it's What Do You Mean, It's Not for Kids?. Indeed, a lot of what we now consider to be for kids ("Little Red Riding Hood", for example) were originally tavern stories adults told each other. They weren't told to children until much later.
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 abound. Oh, and the ending involves the destruction of everything everywhere ever. 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 the late 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 to a young boy with amnesia who's being marked for death as soon as he regains his memory.
Much Victorian literature is like this. While Victorians are stereotyped as a whole century of Moral Guardians, one can find more then a few surprises along the way. Including occasionally things that it would be hard to imagine in a modern children's story.
For example, while Christina Rossetti insisted Goblin Market was a children's poem, it's kind of difficult to ignore the Les Yay, to say nothing of the incest.