Aku no Hana 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 references this in one of the Extra Lessons chapters, where Sakaki admits to being afraid of the mechanical crossing guards at construction sites.
Battle Royale invokes this 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.
Hell even before Griffith is just unnaturally beautiful, especially The Golden Age movies where the artists did their best to make◊ Griffith's face look angelic but alien compared to everyone else.
Berserk (2016), everything the severe backlash from fans comes the fact all the characters are essentially CGI-mannequins. Nobody looks natural the faces don't react and all the "talking" moments feel like someone trying to tell a story in Garry's Mod. There are some moments where 2D animation is used which is a relief when it happens, but those moments are few and far between. The blu-ray DVD release uses more 2D moments and uncensors some the nudity which had Barbie Doll Anatomy before but fans were still unimpressed.
Bubblegum Crisis Tokyo 2040lampshades it, 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.
In Cat Planet Cuties, this is 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 falls smack dab into this trope. Example here.◊
Death Note deliberately aims 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 in a more exaggerated way than the other characters. Given the numbers of fans L has, this backfired.
The creepiest example in the early series, was the Goku doll◊ created by the equally creepy Mr Popo made for kid Goku to train with. The doll is completely silent and just stares blankly at normal Goku with it's emotionless Mr Popo-like eyes and even more creepily when the doll does the Kamehameha he doesn't speak the words just mouths the words. The English dub makes it more creepy by giving the doll raspy noises when he uses Kamehameha instead of saying the words, when the doll dies it turns back into a Goku-shaped mold of clay.
Chaozu was also example of the Uncanny Valley himself when he first appeared, until Defeat Equals Friendship kicked in and he gained more emotions and facial expressions. Considering he was based off Jiangsh (Chinese Vampire) this is very fitting.
Tien has uncanny-ness himself considering his Third Eye and the fact no one else in the series has a third eyeball in their forehead but considering Tien is a rampant Chick Magnet this trope doesn't apply to Tien as much as it does to Chaozu.
There's also a very disturbing example in King Piccolo anime filler, when Goku is in the cave of darkness he comes across a copy of Kami house full of copies his friends. Goku is fooled briefly despite the gang all talking in creepy high pitched voices and acting unnatural.
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 attractive (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.
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 odd example occurs with the original edited English dub. It heavily censors violent scenes, and more extreme wounds on characters are digitally painted out. Unfortunately, the edits over characters make them look really off and don'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 has this 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.
In 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.
Used to a deliberate effect with some of the Stands of the villains. Being an extension of one's self, the more sociopathic characters often have stands that are humanoid but have features that trigger mental alarm bells, not unlike a psychopath's public persona. Some examples are Yoshikage Kira'sKiller Queen◊ who is always seen with an expressionless skull-like Frozen Face, Dio'sThe World◊ that has enormous lips and dead monotone eyes, and Anjuro "Angelo" Katagiri'sAqua Necklace◊ that has a mouthful of fangs and is covered from head to toe in giant eyes.
The Kindaichi Case Files uses thisv 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 are three identical robot girls. Outwardly she seems three ordinary human blonde girls... until you notice her skin is unusually pale, her motions are eerily mechanical, her expressions are completely aloof and unchanging, they are nearly always silent and they never blink. Anybody who sees them can immediately tell there's something seriously wrong with them... before they begin punching holes in walls and shredding things with her razor-sharp hairs.
Most of the human-looking androids Dr. Hell built are sufficiently well done to reasonably pass for humans. An exception is a Kouji-alike android. That robot looks just like Kouji, but it behaves in a different way and it can't speak. It's pretty unsettling because he LOOKS like Kouji but you can say something doesn't fit.
Lorelei kind of averts it. Nobody thinks something is 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 displaying a range of emotions. Minerva thinks they are 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 by Akune in Chapter 134 to describe why Medaka's technically perfect drumming fails to evoke any emotion from her listeners. Zenkichi says it's more like the inverse of the Uncanny Valley, because while her playing is technically perfect it lacks any kind of self-expression, making it come off as inhuman and somewhat disturbing.
In Mekakucity Actors, the intro of episode 9 is supposed to be a cute, heartwarming montage of Kido, Kano, Seto, 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). The redone version for the BD sets, by comparison, is in 2D and does a much better job of trying to be cute.
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.
Sasuke as well especially when he goes off the deep end after he kills Danzo, he goes from pretty boy to freak boy◊ in the space of seconds. This may be a case of Evil Makes You Ugly.
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.
Averted with Buggy the Clown since the only real unnatural thing about him is his red nose and his silly demeanor makes him hilarious and not in the slightest bit scary. But completely played straight with Laffitte◊ whose face doesn't change even when damaged though he's more creepy mime than creepy clown.
Indigo from Strong World is possibly even creepier than Laffitte, as not only does he make creepy exaggerated facial features towards the end of the movie but also catches you off guard since he was acting pretty goofy and harmless at the start of the movie.
Nearly everybody in movie 6 thanks to Mamoru Hosoda's artstyle and used in the context of the story which is very unlike One Piece. The movie while very good became very unsettling for fans, DJ Kappa is especially creepy◊ but he's nothing compared to how horrifying the ending is.
Satori in Skyepeia is just odd, his completely round glasses, high voice and "dumpling"-like body. Satori's boss Enel is mostly normal looking except for his Oh, Crap! moment against Luffy where his face distorted in shock it's quite funny in context but the image alone is bit unsettling.
Fukuro out of all the members of CP9 is just plain weird thanks to his big round body and his vaguely disturbing zipper mouth. Plus there's the insistence he have female voice actor in the anime which just adds to the uncanny. Kumadori is also a weirdo but since he's based off Kabuki theater shown by his appearance/behavior.
Most the villains and zombies in Thriller Bark go straight into Uncanny Valley territory though it's Played for Laughsmostly. The tree zombie is very creepy since it's got a human face stitched to a tree trunk, Hogback and Absalom are very off-putting especially in Absalom case since he's not a zombie but still has a mouth of lion and other "parts". Perona and Cindry are more attractive but have their creepy moments. Gecko Moria looks like outright monster despite being supposedly "human".
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. Fujiora is the same, to Akainu-level creepily realistic.
In Dressrosa three individuals are deep in Uncanny valley thanks to personalty quirks, first is Cavendish or more specifically his evil alter ego Hakuba◊. Sugar of the Domflamingo family mainly due to the fact she's looks like she's 10 when she's actually 22 years old and her sadistic nature makes Sugar very off putting. Dellinger when it turns out he's got More Teeth than the Osmond Family.
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's 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 invokes it 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 the 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 these are depicted by paper cutouts of real images.
Rozen Maiden invokes this with the dolls when they have to act like regular dolls, 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! gives the returning characters from Soul Eater 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.
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 Bakura is actually very cute, then Yami Bakura is VERY much in the valley. Aside from some slight differences, he has the same features as Bakura, 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, small noses, and small mouths start to look unnerving.
Some people have an Uncanny Valley reaction to the "big eye little mouth" appearance of anime and manga characters in general.
A lot of works by Junji Ito thanks to his distinctive art style. It works great for his usual horror works, but it becomes hilarious (and a bit unsettling) when he continues using it for stuff like Cat Diary, a silly comic about his wife's cats.
Nui from Kill la Kill is a deliberate, unique take on this, as her constant Leaning on the Fourth Wall (i.e. leaning on her own Boss Subtitles, stroking a character's hair through a split-screen divider) and frequent Stylistic Suck animation (at one point dodging attacks by having her animation cel rotate around them) add to her general creepiness and the feeling that there's just something seriously wrong with her.