The villainous Gray Agents of Sean Cullen's Hamish X series of novels are described as being deep down in the Valley.
Name-checked in the Mercy Thompson novels. Mercy describes the vampire Marsilia as being in the Uncanny Valley, as she's unnaturally stiff and still and her facial expressions look like she tried to learn them from a book.
The Vord Queen in Codex Aleratries to act human and look like a Cute Monster Girl, but mostly just succeeds in making everyone, even Invidia, want to hide under a bed somewhere.
The queen of The Fair Folk in the Discworld book The Wee Free Men is described as looking subtly wrong, because she's too perfect-looking to be human. It turns out her entire body is just an illusion of what she wants the viewer to see.
Look at her eyes. I don't think she's using them to see you with. They're just beautiful ornaments.
Lords and Ladies, notably during the Queen's confrontation with Magrat when her glamour starts to fail.
Paolo Bacigalupi apparently has a fetish for girls who fall into this category. The most blatant is the titular character of The Wind-Up Girl, so called because she walks in a jerky manner like a wind-up toy. In-story, this is considered remarkably beautiful, but it's somewhat difficult to visualize how this could avoid falling into the Valley in real life. In-story, it sometimes does. It was also a deliberate design feature to make sure that the main character and others like her couldn't be mistaken for unmodified humans.
The human-animal things in The Island of Doctor Moreau by H. G. Wells. Just reading about those things is disturbing. Reading about how they're created even more so, as Wells goes into just enough detail about the processes to be even more freaky.
A Fire Upon the Deep. The female human protagonist is watching a transmission from her homeworld, which has been taken over by an alien with god-like powers. She can clearly see that the human being used as a puppet/mouthpiece is acting strangely, but the aliens with her don't notice anything wrong with him because they're unfamiliar with human body language signals that we notice instinctively.
The Harry Potter series uses the Uncanny Valley to great effect:
If a character acts odd (for example, Ginny's overall behavior in Chamber of Secrets, or teenage Snape walking in a "twitchy manner that recalled a spider" in Order of the Phoenix), keep your eye on him or her. And then, of course, there is the Inferi, which deliberately invoked this trope (because there is absolutely nothing right with a walking corpse). The way Voldemort is characterized in the movie also invokes this trope.
Luna Lovegood is described as having wide, buggy eyes that she blinks less often than one normally would. It helps to augment her strangeness, though she's also a sympathetic friend of the protagonists.
Another one would be Ollivander. It's mentioned in his introduction that he almost never blinks and Harry is creeped out by him.
Played straight in Neal Asher's Cormac novels with the Golem androids. Early in the series most Golem androids are absolutely perfect in their humanoid design, with god-like strength and god-like beauty. Humans are usually pretty disturbed by them in their perfection because it makes the androids feel LESS human, since real humans aren't perfect. Furthermore most non-combat Golems have inhibitors which stop them using their joints in impossible directions and from using strength far greater than even an enhanced human. Subverted when later models have purposeful imperfections (moles, limps, idiosyncrasies) to make them feel more human (but are still quite capable of tearing people, and other androids, limb from limb).
In Jane Eyre, Jane is the only person who recognizes that something is wrong with Mr Mason: "...I like his physiognomy even less than before: it struck me as being, at the same time, unsettled and inanimate. His eye wandered, and had no meaning in its wandering: this gave him an odd look, such as I never remembered to have seen. For a handsome and not unamiable-looking man, he repelled me exceedingly...".
The Strange Case of Dr. Jekyll and Mr. Hyde: Utterson says that Mr Hyde's appearance gives the impression of deformity without having any. People who look at him dislike him immediately without quite understanding why, though by the end it's clear that his underlying evil causes the reaction rather than any physical property.
Occasionally this trope's effects are felt in Niven's Ringworld novels, as the many hominid natives fall short of being Human Aliens. Usually it's the ones that are already creepy (ghouls, vampires) which give people the willies when they move their shoulders more loosely than expected or are found to have too small a skull.
Also part of the reason our Abusive Precursors are so, well, abusive. Our social system is horrifically twisted due to its rejection of Protector-stage rulers, and we just smell so incredibly wrong.
Played with in the Gaea Trilogy, in which a race of obviously-nonhuman alien centaurs, for reasons that make sense in context, sport genitalia identical to those of humans. This single feature's similarity invokes the Uncanny Valley effect because the rest of the body is so strange.
the alloy of humanity that softened the godliness of the youth was lacking in the features of the stranger, awful and immobile in their beauty.
Scott Westerfeld seems to have a talent for creating things that are Uncanny with a capital U.
The Pretties from the books series Uglies; they're literally perfect with symmetrical faces and all, and they all look very nearly the same. Then there's the specials who add a whole new level of creepy with their "cold beauty".
Lampshaded in So Yesterday. A special effects whiz explains that the human face is the hardest thing to animate convincingly because humans spend almost all of their time reading faces. If it's even a tiny bit off, we won't accept it.
... at last he [Quasimodo] said, shaking his heavy and ill-formed head,—
"My misfortune is that I resemble a man too much. I should like to be wholly a beast like that goat."
Mostly averted in C.L. Moore's story "No Woman Born". When a noted dancer and actress has her brain transplanted into a robot body after an accident that nearly kills her, she is still able to convey the same sense of beauty, grace, and charisma as before, although she needed to practice moving and talking in her new body before presenting herself to the public. The scientists who worked on her new body decided to give her a blank metal face to avoid the almost-but-not-quite human effect and designed the body to be flexible enough to dance as gracefully she could before, and this is justified in that humans rely on auditory and kinesthetic cues such as voice, gait, and personal mannerisms for recognition, not just appearance. Only at the story's very end, when she lets down her guard for a moment does her voice start sounding flat and robotic, instead of resembling her original body's voice.
The short story Stairway to the Stars by Larry Shaw, has this concise explanation: "It — he? — looked almost like a man, and that only made the difference worse."
In Rick Griffin's Argo, androids are usually designed to look like Petting Zoo People to avoid this trope, so that humans would be less intimidated by them.
Kellhus from Second Apocalypse. He is completely emotionless, lacks any empathy and is utterly, ruthlessly rational. He can manipulate people by perfectly simulating emotions and normal human interaction. However, at one point he makes a mistake with one character. He takes just a split-second too long to respond to a question, during which his face just goes utterly blank and all emotion leaves his eyes before suddenly smiling and continuing with the conversation. The effect is described as extremely disturbing.
Invoked in Jugend Ohne Gott, a book written during the Nazi regime, about the indoctrination of the children. The main character (their teacher) constantly comments that several of them stare at him blankly, like fish.
In The Pale King, there is something very, very off about Shane Drinion. His odd speech patterns, lack of emotions, facial reactions, or sense of humor make him seem inhuman. There's also the fact that mosquitoes avoid him, he can levitate if he concentrates hard enough on something, he keeps a perfect record of his conversations, and that he can't leave the room without Keith Sabusawa. None of it is explained.
Why is this◊ cover for the Haddix book Turnabout so creepy, you may ask? If you didn't notice (some won't), half of the face is young when the other is old, effectively creeping us all out.
Coraline: Some of the pictures in the novel - especially the picture◊ of the Other Mother with a bug in her mouth.
The GMO's and their offspring exhibit a subtle version of this in Jacqueline Carey's Santa Olivia and its sequel. For the most part they look normal but its frequently mentioned that when making physical contact for most people there is something subtly wrong and unnerving about them. Their inability to feel fear also means that in some situations their behaviour is off in ways that others find unnerving.
Raptor Red's protagonist and main viewpoint character is a female Utahraptor of the Red-Snout species. A rival species, the Yellow-Snouts, evoke an Uncanny Valley reaction in her: their courtship dance is almost right, but the differences in the motions and in the colour of their snout-band repulse her.
In A Song of Ice and Fire, Melisandre is beautiful, but there is also something off about her. Most men are too afraid of Melisandre to want to sleep with her. The only one who does sleep with her is only doing it because it's part of a Blood Magic ritual.
H.P. Lovecraft frequently describes degenerate humans and not-really-humans as looking distinctly off and inherently disturbing, such as the people of Innsmouth, who have fish-person blood. It can be seen as applying this trope, although at least in the more extreme cases his main idea may be not almost-humanness so much as the inherently disturbing eldritch shining through; if there was more of it, it would just be even more disturbing. On the other hand, Lovecraft had fears of degeneration, of the human being too close to the not-human (in "Facts Concerning the Late Arthur Jermyn and His Family", this is played as the ultimate horror), which naturally implies a form of this trope.
Naar from Lone Wolf doesn't really have a true physical form, but the one he favors in his inner sanctum is a grotesque misshapen thing. The trait that shocks Lone Wolf more than the others? The dark god has the eyes of a man.
In The Witcher novels the elves are described in terms that suggest this trope. On one hand they are extremely beautiful in general terms. On the other, at closer inspection their eyes seem unnaturally large, while their teeth seem too small to their mouths, like adults who still have baby teeth, and they also lack the distinct canine teeth. In result, many humans find elves freaky and disturbing-looking, although the actual reasons for the mutual Fantastic Racism have a bit deeper causes.
In The Wheel of Time, the Myrddraal are some of the most human-looking Shadowspawn (barring the gholam, which was created to be able to perfectly mimic humans in order to fulfill its function as an assassin, and only turns monstrous when it uses its Rubber Man powers). They're also, however, the most disturbing. It's partly their skin, which is a bit too pale. It's partly the way they move, which is a bit too fluid and makes them look like their joints don't hook up quite right. It's partly the fact that their clothing is always perfectly still, regardless of factors like wind. It's partly their expressions, or lack thereof- Myrddraal never smile and rarely show any emotion that isn't cold-blooded sadism, and there's no noticeable variation in personality between individuals. Oh, and when they lower the hoods of their Black Cloaks, it becomes obvious that they don't have eyes, just smooth skin where eyes should be... but they can still see. Taken all together, they're far more horrifying than the traditionally monstrous Trollocs.
Shapechangers pretending to be humans have this effect in The Power of Five. Of the few that are mentioned, not a single one has maintained their deception for any length of time: One lets his disguise slip when he meets Scarlett, the other has a freakishly round head, one can't speak, one doesn't notice cutting his own thumb off, and one doesn't notice an enormous insect crawling over his eye. The best impersonation so far has been "Audrey Cheng", and even it gave the game away when it forgot to eat. Scarlett rumbled it when she realized the only time she had ever seen "her" express hunger was looking at a fishmonger's slab.
The dolls in The Dollmaker appear human (to varying degrees), but they are consistently described, in both appearance and action, as disturbingly other.
In Those That Wake, Man in Suit evokes this trope, leaving the characters confused and frightened by their inability to describe him.
Perelandra feature the Un-Man, who is essentially an animated corpse, but he gets even more creepy when you think about what it is that's animating him.
The description of the vampires' body and skin when one thinks about it. Their skin is beyond eerily pale and their bodies are as hard as rock or diamonds, with the corresponding temperature. Meaning, they are cold as ice to the touch. Their temperature never rises, so no matter how long they may be in a hot climate, they remain like ice.
Breaking Dawn had an unintentional example with Renesmee. She's supposed to be seen as cute and endearing, but she's described as having teeth as soon as she's born and her unnaturally fast growth also has her extremities be "lean" and "almost adult-like" in length when she's only a few weeks old, making her appearance come across as that of Noodle People. Renesmee's also supposed to have an adult intelligence, but she still does very childish things like biting people - coupling that with the adult mind makes her actions feel very unsettling.
In Goldfinger, James Bond describes the title villain in this manner. His unease comes from Goldfinger's apparent lack of symmetry—he's like a collection of features that never quite add up to a satisfying whole. His attempt at recreating the man's face on an Identikit machine only adds to his distress.
A couple of novels have this apply to the Doctor, who is, after all, a Human Alien. One instance is after he's fainted at a sideshow:
In Hugo’s arms, the Doctor hung bonelessly limp, as if he might suddenly flow to the floor in a puddle. Anji had never seen a human body sag like that; no human being had that sort of muscular-skeletal frame. For a frightened instant, she felt more kinship with the man with no limbs than she did with the Doctor.
And one even has a character feel something of the sort applies to the Doctor's human companions, who are fairly ordinary-looking 20th-century Earthlings, as said character is a member of a much more homogeneous future human society:
Their variegated pigmentation, certain small inconsistencies about their facial and bodily forms, evoked a terror in me in some quite other part than if they had been merely monsters. We do not look at a Vlopatuaran land-going octopus or a Wilikranian aerial predatiger and feel quite that fear, I fancy; it takes a man like us in most but not quite, deformed in ways we simply cannot expect, to in this particular manner fright us out our lives.
In-Universe in The Clockwise Man. Due to Melissa's information on how humans looked being inaccurate her face is described as a "parody of humanity", with eyes that seem too human.
"Everyone who saw her at the police court said she was at once the most beautiful woman and the most repulsive they had ever set eyes on. I have spoken to a man who saw her, and I assure you he positively shuddered as he tried to describe the woman, but he couldn't tell why."
Shelly from The Troop is constantly described as "insectile" or even less pleasant adjectives. One kid even thinks of him as "something" at one point. Of course, Shelly is a closet sociopath, so it may be the other kid's survival instincts.
"Yes; she had quite a court around her. She would be called very handsome, I suppose, and yet there is something about her face which I didn't like. The features are exquisite, but the expression is strange."
In-universe in the Sector General novels. One of the series's main alien cultures is the Kelgians, who are human-sized furry mammalian caterpillars, with constantly mobile fur that expresses their emotions. In one of the later novels, a character is introduced from a different species, which has a similar body plan but black, immobile fur. Apparently he looks to Kelgians like their equivalent of a Humanoid Abomination.
Any book dealing with the speculative evolution of humans like Man After Man and All Tomorrows is bound to contain this as they always contain the surreal results of a world where most wildlife (alien or earthly) is descended from humans. All of them still retain their ancestors' traits to an extent.
Most of the anarchist Council of the Days in The Man Who Was Thursday have something fishy about their appearance (e.g. Monday's lopsided smile, Saturday's Sinister Shades or Friday's disquietingly great age) which makes the protagonist deeply uncomfortable. The worst of all, however, is Sunday, mainly because the man is so damned big — he is tall and overweight, but he seems moreover to be out of scale with his surroundings, like (in the narrator's words) a statue carved larger than life-size.
Serdra in The Silent War is this in-universe. She is an immortal in her 130's, with a youthful face yet somehow radiates age. Her nearly emotionless demeanour and constantly intense gaze disturbs people, and she tends to let her pupil do the talking to muggles.
In Frankenstein, this is what triggers Victor's near-immediate rejection of his creation. Victor had selected all of the Creature's body parts to make him as physically imposing and attractive as possible. What he ended up with was a sallow-skinned, sunken-eyed, varicose-veined hulk of a man with serious anger management issues. True to form, the trope kicked in as soon as it started moving.
Main/Faust: This illustration of Mephisto by Harry Clarke.
In Only Ever Yours by Louise O'Neill, women can no longer be born naturally. They are bred in laboratories as future wives and prostitutes to serve men; and are engineered to be as physically perfect as possible. When protagonist freida and her classmates first meet the Inheritants (the group of boys they were designed for), freida notes the sharp contrast between the naturally born and physically diverse boys, vs the manufactured and artificial appearance of the girls.