Aku no Hana: The anime adaptation is a rare example of Rotoscoping in the medium. Because of this, some of the characters look... off from real-life people, let alone their original manga designs.
Attack on Titan uses this to absolutely brilliant and chilling degrees, with the designs of the Titans. The majority are deformed humanoids measuring anywhere between 4 - 15 meters in height, with Barbie Doll Anatomy and creepy, cheerful smiles that never waver regardless of being blown apart or in the midst of devouring their victims. This is further used with the unique, deviant types encountered throughout the course of the story. Eren's Titan form has pointed ears and a skull-like face, while Ymir's Titan form looks animalistic with shark-like teeth, claws, Creepily Long Arms, and fur sprouting along its shoulders. As a result, both look more like traditional non-human monsters in a reflection of their being on the side of humanity. The Armored Titan has an almost robotic appearance, due to the armored plating covering its body and is less creepy than the Colossal Titan and the Female Titan, who are essentially skinless but otherwise very human in appearance. This seems to hint towards Reiner's Becoming the Mask, in contrast to the more more ruthless Bertolt and Annie.
Some viewers and readers claim that the human characters can come across this way as well, especially when pulling off dramatic facial expressions.
This is somewhat justified/lampshaded by resident genius Armin - he notes that in order to win against monsters, you must be able to give up your humanity.
Azumanga Daioh: Referenced in one of the Extra Lessons chapters, where Sakaki admits to being afraid of the mechanical crossing guards at construction sites.
Battle Royale: Invoked for Kazuo Kiriyama. He was deliberately drawn with no reflection in his eyes, and while barely noticeable, it still manages to give his face a look beyond creepy.
Invoked when Guts and Puck encountered Rosine's minions for the first time. They looked really similar to Puck's elf kind, he said.... but there was somethin' off about them.
It's safe to say that Griffith is now in the valley, especially now that he has been reincarnated. He is now so beautiful that he both awes and frightens people at the same time and the fact that he's a Humanoid Abomination.
Bubblegum Crisis Tokyo 2040: Lampshaded, as one of Linna's coworkers complains about the creepiness of the newer, more human-looking Boomers.
Busou Renkin: While most homunculi look convincingly human until they transform into spawns of the devil, Papillon's human persona in particular just looks odd. His eyes are always fixed on a lifeless stare bordering between condescension and rage, regardless of the actual emotion he's trying to express. His pale skin just makes him more unsettling. He's one of those people you'd actually feel afraid to even approach.
'Cat Planet Cuties'': This was one of the reasons why the Assistroids are in their current form. The last generation were Ridiculously Human Robots that were normal size. Due to this, the Catians couldn't see them as "Tools", and a war was fought till the current generation of Assistroids was made.
City Hunter 91 and Angel Heart use realistic, sketch-like art style to depict main characters' serious/dramtic faces which easily come off as uncanny. The worse offenders are Ryo and Kaori themselves in Angel Heart anime, where their voice acting bounces all over the place and doesn't match the expressions, making the issue even weirder.
D.Gray-Man: Level Four Akuma intentionally fall smack dab into this trope. Example here.◊
Death Note deliberately aimed for this with L's design, including his rather unhealthy, pale skintone, huge eyebags under his bulbous eyes and his facial features and expressions overall being drawn more 'goofy' than with the other characters. Given the numbers of fans L has, this backfired.
Dragon Ball Z seemed to attempt to invoke this with androids 16, 17 and 18, by giving them steel-blue eyes, facial features very different from the series' norm, and (in the dub) inexpressive voices. If this was an attempt at the uncanny valley, it failed, as both 17 and 18 are almost universally considered adorable (and 16, while not exactly a looker, did not have the repulsive qualities that the uncanny valley is known for).
This could actually be considered an aversion, especially in 17 and 18's cases - their appearances, character bents, and personality traits, including the way they dress, actually make them seem like the most human of all the characters to certain fans. (This is virtually guaranteed for viewers influenced by other anime.) In fact, the closest android to this trope is Dr. Gero's bleach-white-skinned companion 19 - and since Chaozu beat him to that punch, his face is often compared to marshmallows.
Chaozu was an example of the Uncanny Valley himself when he first appeared, until Defeat Equals Friendship kicked in and he gained more emotions and facial expressions.
Although if you think about it, this does put them back into the valley in a meta sort of way. The most humanlike-looking characters are in fact cold, lifeless machines. Then again, this part's probably up to the viewer.
Funnily enough, Toriyama originally created 19 and 20 to be the main villains of the Android arc, in a portrayal that would've definitely fit the trope, but the editor didn't like them. So Toriyama made the backstory of 20 actually being Dr. Gero himself, then created 17 and 18 to play in the valley instead, adding 16 a bit later on. The editor still didn't buy it, but Trunks had already been shown confirming them by appearance as the scourges of his time. Thus the random killing sprees were left up to the ones in his timeline, while standard-timeline 17 and 18 were portrayed more like the human teenagers they appeared to be as Toriyama designed a new villain. The result was Cell, who didn't look remotely human (until he crossed the Bishonen Line, anyway).
An American example occurs with the original edited English Dub. It heavily censored heavily violent scenes, and more extreme wounds on characters would be digitally painted out. Unfortunately the edits over characters made them look really off and didn't mesh with the animation at all.
Franken Fran: Fran Madaraki is a Frankenstein-style creature stitched together from dead body parts. She has visible stitching on her face and her eyes are usually drawn to look tired and lopsided.
The Geisha-gynoids could hardly be mistaken for humans and are clearly artificial. However, their staggering mechanical movements and speech have just the slightest trace of humanity, that makes them downright creepy. It doesn't help that they rip people's heads off.
The scientist from the forensics lab. She seems like a highly cynical, chain smoking, but overall laid back older women while talking with Togusa, until he leaves and she takes her face off and plugs cables into her eyes.
The Korean festival parade also touches the trope, though it doesn't cause real discomfort.
Kim himself, and his whole house as well. He had his brain put into a cybernetic body that was shaped and moved like a wooden puppet on strings. To Kim, the deepest point of the Uncanny Valley is the closest any being can come to perfection. As a result, his whole Big Fancy House is full of human-sized dolls, puppets, and robots, turning it into a Doll Houseof Doom.
The Tachikomas discuss the trope, musing that the reason they are allowed advanced AI is because they are not humanoid, and that advanced AI in an android would creep humans out.
Proto, who just happens to be an advanced AI in an android. Even before this is revealed, there's clearly something... off about him. This is likely intentional.
Gokujou!! Mechamote Iinchou: In this half-2D, half-CGI anime, this is aaaalllll over the place. The animation switches from hand-drawn to cel-shaded CGI without warning, the characters, when in CGI-mode, can't even blink very well, and can't move their eyes—in order to face another direction, they have to turn their entire head.
Later episodes seem to use the CGI a bit better, though the non-human characters still look terrifying.
Hen: The artist's grasp of human anatomy can get a little loose at times.
Ijime, a short anti-bullying OVA, has an art style that falls deep into this trope. You have been warned.
The Kindaichi Case Files: Used as a plot point in "House of Wax": The killer intentionally makes wax statues of his guests that are fantastically detailed, but look a little... off. This is so that during a series of crimes when it appears that the wax figures are being set up to resemble the scenes of people who will be found murdered, the murderer can pose as a statue using a mask, and no one will examine it too closely since it so clearly looks inhuman.
Mazinger Z: The Gamia from the original manga and Mazinkaiser were three identical robot girls. Outwardly she seemed three ordinary human blonde girls... until you noticed her skin was unusually pale, her motions were eerily mechanical, her expressions were completely aloof and unchanging, they were nearly always silent and they never blinked. Anybody saw them could immediately tell there was something seriously wrong with them... before they began punching holes in walls and shredding things with her razor-sharp hairs.
Most of the human-looking androids Dr. Hell built were sufficiently well done to reasonably pass for humans. An exception was a Kouji-alike android. That robot looked right like Kouji, but it behaved in a different way and it could not speak. It was pretty unsettling because he LOOKED like Kouji but you could say something did not fit.
Lorelei kind of averted it. Nobody thought something was amiss with her.
In Shin Mazinger Zero, Minerva-X -formerly a Humongous MechaFem Bot- is a Robot Girl. Although she is somewhat unsettling, she is less creepy than the Gamia (moreover, the Gamia had lost most of her Uncanny Valley factor due to display a range of emotions. Minerva thought they were STILL blatantly blunt and obvious, nonetheless). Maybe because even if she does not seem completely human, her actions and reactions are pretty human-like.
Medaka Box: The term "Uncanny Valley" is name-dropped in Chapter 134 to describe why Medaka's technically perfect drumming fails to evoke any emotion from her listeners. Zenkichi actually says it's more like the inverse of the Uncanny Valley, because her playing is so perfect that it comes off as inhuman and somewhat disturbing.
Mekakucity Actors: The intro of episode 9 is supposed to be a cute, heartwarming montage of the orphan trio and Ayano growing up together, but it's kind of spoiled by the CGI models, particularly the faces, which are creepy as hell (especially when they smile).
Naruto: Even though Sai is actually a human, he has the inhuman feel of a robot, mostly because he's effectively emotionless. His vampire tan doesn't exactly help.
The Six Paths of Pain are merely corpse puppets, controlled by Nagato. When they fight, all of them, except Deva Path, Nagato's go-to body, and the corpse of Yahiko, have blank, expressionless faces, usually. The anime goes further and makes them incredibly pale.
Later on in the series, we get the Edo Tensei shinobi. They're effectively zombies. When being fully controlled by Kabuto/Tobi they become emotionless and fight with blank, expressionless faces. Doubly so for the revived jinchuuriki who are being directly controlled by Tobi. Like the Six Paths of Pain before them, they are merely very powerful corpse puppets. Note that In-Universe, these shinobi are all identified by their blacked-out irides and cracked, pale skin.
Kaworu's appearance caused this reaction in a lot of viewers.
The Mass Production Evangelions from End. The masochistic cyborg harpies who are The Faceless except for their ever-smiling bright-red lips just get to people.
Lilith to an extent as well. There's something about a crucified humanoid being that resembles a bloated corpse and with a mask that gives it the appearance of having no face at all that tends to creep some fans of the series out.
One Piece: Due to the fact that the admirals are based off of famous Japanese actors this can happen. While the first admiral shown, Aokiji, does look like a normal character, Kizaru is slightly more realistic, and Akainu doesn't even look like he's part of the show, looking exactly like the actor.
Parasyte: The titular monsters, while usually looking human, never blink and have very limited understanding of facial/emotional subtleties that place them quite firmly in this trope. They also are drawn with slightly elongated eyes with sharply pointed ends that give their faces a distinctly inhuman aspect. Even scarier is that near the end, when police start using these attributes to recognize and kill the parasites, they occasionally kill ordinary (but crazy) humans by mistake.
The protagonist also slowly starts slipping into this as time goes by.
Shinichi (with a sheepish grin): "If you treat pigs and cows as equal beings... then we're eating their slaughtered corpses. So don't be so afraid when someone dies."
Perfect Blue: Mima goes through a journey filled with all kinds of things nightmarish throughout the movie, and while most of the character designs lean toward realistic, there are two notable exceptions: Me-Mania, who is obviously creepy-looking from the start, and Rumi, who, like him, has eyes that are too widely spaced.
Ponyo on a Cliff by the Sea: Granmanmare, due to her design being slightly more realistic than the traditionally Miyazaki-esque characters that surround her.
Princess Mononoke: Invoked with the Deer God/Forest God. A deer with a vaguely mask-like human face that's perpetually smiling instead of normal deer-head, and a veritable bush of horns growing on it. And from side he looks like a deer with front half of its head cut off.
Walpurgisnacht. She's a giant, upside-down clockwork harlequin doll with no facial features except for lips. She's obviously not human, but just human-doll-animatronic-looking enough to be quite creepy.
Witches as a whole, really. While the rest of the characters are drawn and animated in Ume Aoki's style, the witches are each given their own unique styles. Gertrud, the first Witch with a proper fight, has a deformed rosebush for a "head" and butterfly wings that move with kind of a stop motion quality. Both of which are depicted by paper cutouts of real images.
Rozen Maiden invokes this with the dolls when they have to act like regular dolls, and is also shown in the first season's opening. Otherwise, they're just Moe.
In the manga, when Suigintou and Micchan encounter another creator's attempt at making a living doll, they find it unsettling.
Played with in an interesting way in Saber Marionette J. For the most part the saber marionettes act as Ridiculously Human Robots, but on two separate occasions one of them has something happen to her 'maiden circuit' which controls their emotions. They then nosedive instantly into Uncanny Valley territory, marked mostly by their vacant stares and completely lack of movement except when prompted.
A common criticism of Crystal is that it tries to copy the manga's artstyle too closely resulting in anatomy and facial issues.
Crystal's version of Chibi-Usa is basically an adult head running around on a toddler body. Every scene with her just screams wrongness.
Shirokuma Cafe fall into this trope with its animal characters as they are drawn in a rather photorealistic looking style.
Soul Eater Not!: The returning characters from Soul Eater were given a cutesy and more realistic Moe redesign that just looks off and wrong. This is considered one of the main reasons the show didn't do very well.
No-face deserves special mention. Just looking at that blank expressionless face on the pale, ghostly body is enough to give you the willies. Observe.
Squid Girl: Eiko pulls out a really creepy looking doll in episode 11 of Season 1. She later finds the doll's partner, who's broken up a little and freaks out all the girls looking for it.
Suicide Island has an art-style that, in general, has this effect on the humans. Overall, the scenery is done well, but the humans are drawn a bit sketch-like and the tendency of having an emphasis on big noses makes them feel a little unsettling.
The cat family featured in the 1947 anime Suteneko Tora-chan look a little creepy with faces that mostly look like real faces.
Tiger & Bunny episode 15: Cis seems to have been deliberately made to look and act just slightly off.
In Time of Eve, the robots are all clearly identifiable and do not act human in the slightest. However, any notion of treating robots as human, or that robots can act human, are vehemently opposed by society, illustrated by the constant anti-robot rights ads that play on TV.
Most of the characters in one The Wizard of Oz adaptation use cartoony designs, which makes characters like Dorothy◊ look a bit off.
Actually referenced offhandedly in The World God Only Knows. One unique girl is trying to make a 'human' out of a remote controlled box, but people laugh at it. Keima draws a little smiley face on it and adds a cute note, and suddenly people are helping out. The girl decides to put a mannequin head on it to make it even more human... and it creeps people out to see a box with a human head on top roll through the hallway.
As a whole, Bakura fits in the valley. If you think that Ryou is actually very cute, then Yami Bakura is VERY much in the valley. Aside from some slight differences, he has the same features as Ryou, but there's something very wrong with his expressions... also, Yami Marik would look okay if it weren't for the veins that become more and more prominent on his face, and the way he sticks out his tongue.
This trope can occur when works drawn in a general anime/manga style are shaded very realistically. Once the picture begins to look like real life things like enlarged eyes, missing noses, and small mouths start to look unnerving.