Rotoscoping and Motion Capture both tend to fall under this category since the two techniques require tracing over live-action (2D in the former's case and 3D in the latter's case) to make the characters move and/or look realistic. Unless the characters in question are stylized or are fully detailed (such as including proper shading, textures, and outlining), there's pretty much no avoiding falling into this trope when using either of the two.
This trope goes back as far as Disney's Snow White and the Seven Dwarfs film (and earlier if you count the Silly Symphonies short "The Goddess of Spring"). In the original, Snow White is Rotoscoped, while other characters are not. As a result, she is the only one in the movie who looks unnatural. Ironically, she is the only detail of this ground-breaking film that looks old-fashioned even though rotoscoping was considered cutting edge technology at the time. The Seven Dwarfs are recognizable instantly, but Snow White fades into the background when she isn't singing or dancing. Prince Charming, by the same technique, manages to be even more of a blank than Snow White, partly because he wouldn't have a personality if you gave him a rocket-powered step-ladder.
The Blue Fairy from Pinocchio is another early Disney example. Again, due to being rotoscoped, she ends up looking almost like an actual person when compared with the more cartoony looking humans in the film. That may be intentional, however, given that she is a fairy, and supposed to look inhuman.
Dumbo is yet another early, but intentional Disney example. The film seems to mostly avert this due to its simple and cartoony style compared to most Disney animated features, but its invoked with the disturbingly realistic Horus/Illuminati-like eye that appears during the already creepy Pink Elephants on Parade segment when the belly dancing elephant dissolves. Made especially jarring when comparing this to anything else in the film.
The 2012 Disney short "Electric Holiday", done in partnership with Barney's New York (a fashion company) seems innocent enough, until the scene with several Disney characters at a fashion show where their heads are placed on skinny human bodies, even in the case of Mickey and Minnie Mouse, and Daisy Duck. See for yourself here.
Many of the human characters except for Penny in Bolt have a pinched, waxen look to their faces ranging from slightly weird to just plain creepy, making them look more like plastic dolls.
The Hunchback of Notre Dame: The way Quasimodo is made to look Ugly Cute without subverting the original premise seems to be due a to clever, deliberate aversion: Draw all the characters in a fairly realistic way, draw Quasimodo as very deformed in the same realistic way, but make him so deformed that, since he's still animated rather than real, he's left on the far side of the valley... except in-universe, of course.
On the other hand, the CGI background crowd looks somewhat weird in comparison to the traditional animation most of the film uses.
Rapunzel from Tangled and especially Anna and Elsa from Frozen have invoked this reaction. Their large eyes and barbie-doll complexion and thin proportions either make them incredibly adorable or awfully horrifying. The latter two are infamous for invoking this reaction when images of their designs were leaked. Fans were rabid and thought they looked absolutely terrible. The designs were later revised, and when they were shown animated, most warmed up to the sisters, though many still consider them creepy.
Invoked in Wreck-It Ralph: Turbo, the lead character in Turbo Time, is a game character that's human, but due to the graphic limitations of his 8-bit game, he has grey skin, an oversized head, bright yellow teeth (which are all exactly the same size and shape, and perfectly straight so that they all seem to be one piece), glowing, sunken yellow eyes ringed with dark circles, a pudgy body, and skinny limbs, giving him the appearance of a zombie. No wonder his game lost popularity when Roadblasters arrived.
Up to 2006, the studio's animation was pretty infamous for this, promoting the phrase "Dreamworks face". This is very clear for the characters in◊ Antz.
The producers of Shrek intentionaly dialled down the realism of Fiona's skin, because the animators reportedly felt a bit like they were animating a corpse.
Eris from Sinbad: Legend of the Seven Seas is an interesting example. She sort of tiptoes across the valley by looking decidedly scary with her gray skin and yellow eyes, but being very, verysexy. In a couple of scenes she is goosebump-inducingly creepy, yet awe-inspiring in others. Her character design also varies extremely from the other characters in the film, which makes her stand out even more.
The human characters from Monsters vs. Aliens, due to the extreme detail rendered into their skin.
An intentional example in Penguins of Madagascar: Dave, when posing as Dr. Octavius Brine, makes some movements that are impossible even for a cartoony human, like walking on the ceiling, leaning forward almost to the ground, and stretching his arms to extreme length. These all indicate his true identity, but the humans are still fooled by his appearance.
Pixar has this for the human characters in its early films (from Toy Story to Finding Nemo), but they worked around it by avoiding direct shots of them, so a major reason for some strange settings was to feature characters who would look less odd as CG characters. The human cast of The Incredibles and Ratatouille are probably the most realistic, but they avoided the Valley by having cartoonish proportions. In WALLE they try to avoid it, but there are some people who found the live-action scenes deeply disturbing. The CG background and cheap props only make it worse, particularly in comparison to the detailed post-apocalyptic wasteland (which possibly explains why they've never done it again since). They managed to avert it by the time Toy Story 3 came out.
The early short Tin Toy is infamous for this. Everyone remembers the horrifying-looking baby. By the time Toy Story rolled around, they at least seemed like they were starting to get that humans didn't need to be fully realistic. They hadn't figured that out yet in 1988, and not only was the baby◊ in the short creepily almost-realistic, but it got even worse compared to the cartoonish toys which were the only other characters.
Merida from Brave has come under fire for having a bizarrely shaped head and rather beady eyes. The other characters are less stylized.
The animation in some of their later films, like Inside Out, is so realistic and hyper-detailed it can cause this reaction in some viewers. The Good Dinosaur in particular got a handful of complaints for having dinosaurs and humans with cartoony proportions interacting in virtually photorealistic environments.
Spirited Away invokes it with passengers on the Afterlife Express. 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◊, or maybe even worse when he becomes monstrous and gains a mouth full of teeth and bulbous body... but his mask-like face stays the same. Hell, Spirited Away invokes this everywhere, from the anamorphic animals to the "regular" humans who look completely alien◊ compared to Chihiro, the justification being that most of them are spirits.
The Adventures of Tintin: While it mostly averts it by having its characters more stylized and cartoonish, Tintin himself has a more realistic face, and is thus more off-putting for not looking fully lifelike.
Animal Kingdom: Let's Go Ape: Being an animated film that uses motion capture, the apes can look creepy. As this review points out, they have "weirdly humanoid figures" and "recognisably human faces".
Mostly averted in Beowulf since everything is motion-captured in real-time, and the character design and graphics are similar to those from a modern video game. Most of the extras however (where they didn't bother to Mo-Cap the faces) tend to fall squarely in the middle of the Valley.
A Christmas Carol (2009), featuring Jim Carrey as the voice of Scrooge and the three ghosts. The motion-capture and general animation style can make every character fall into this, but the Ghost of Christmas Past gets it the worst, especially when its face rapidly cycles between people Scrooge knows.
Coraline deliberately sweeps the valley to induce fear.
The human characters mostly avoid it, considering that they aren't very realistic, but they are realistic enough to make the ragdoll versions of themselves fall into this trope. In general, taking emotion and soul out of a face is a keen way to achieve the Uncanny Valley, so in this case taking out one of the most expressive parts of the face, the eyes, was a good strategy.
The stop-motion in the Otherworld is slightly off, doing things like having single frames where background objects suddenly jump around, just enough to be unnerving.
The moving men◊ at the start are almost as stiff and horrifying as the Other Mother.
Mr. Bobinsky has blue skin, freakish long legs and a big gut, and he's supposed to be a normal human. There's some justification, as the background information states he was part of the Chernobyl clean up crew, which may explain his appearance.
As the Other Mother's illusions start wearing off, the Other Father begins looking increasingly melty (for lack of a better word). And that's without mentioning the Other Mother's true form.
The characters in Corpse Bride aren't nearly as appealing for the most part as the more cartoony ones in The Nightmare Before Christmas because of this trope. The more subtle expressions (as opposed to the more convincing stylized ones) end up looking especially creepy sometimes. They were able to achieve these more subtle expressions by replacing the industry-standard replaceable heads with precision-crafted clockwork heads. However, not only did this make the animation process longer and harder, but it also caused one of the animators to have nightmares of resetting his own expressions through clockwork mechanisms.
The use of puppets in Fantastic Mr. Fox could be considered this trope. Their highly detailed fur and eyes make their cartoonish movements come across as unsettling, and the close-ups of their faces in particular betray the fact that these puppets were not designed to pull off subtle facial expressions. Animation with animal characters generally avoids full-on front shots of the face due to the foreshortening of the muzzle looking somewhat strange from this angle (as opposed to the relatively flat faces of humans, which can be seen from this angle without features seeming altered). However, plenty of those shots are used in the movie, as they fit with Anderson's style of carefully composed, heavily symmetric shots. And some look creepy as cuss.
The failure of the movie was partially blamed on its characters being right in the Uncanny Valley. The rest of the blame could be chalked up to boredom. Somehow, the female lead, Aki Ross ended up being placed in a Maxim Magazine's "hottest women" list. Nice body aside, her skin looks like porcelain. Creepy. Especially given that "skin like porcelain" is supposed to be a compliment.
At the time of its release, the studio had hoped to use the Aki Ross "virtual actress" in other productions. This obviously never happened. Ironically, test footage for the movie, released several years before the finished movie, showed an early version of Aki that is somewhat more realistic yet at the same time less uncanny valley-esque.
Another factor contributing to the film's uncanniness is the motion. While the characters' faces are well-animated (if nonetheless off-putting), the movements of their bodies are stiff and awkward, with a relative absence of motion blur simultaneously causing them to appear unnaturally smooth and fluid. The high level of detail on the characters' faces also jars heavily with the relative lack of detail in their bodies/clothing.
Cloud suffers from this rather badly, which is not surprising, as the animators have admitted that he was one of the most difficult to make look realistic. Granted, he does appear passable in◊ some shots◊, but for the most part, he just looks off due to his extremelypale face◊ and angular features juxtaposed on a muscular body which doesn't quite◊ match them◊. There's also the weird stiffness◊ to Cloud's face where it remains completely static and unexpressive during the high-octane action scenes, and the frequent use of extreme closeups certainly doesn't help matters.
Barret's face is also weird◊. While he's not quite a Scary Black Man, he's still quite off-putting due to his features being overly cartoonish, as if his model was created by someone who has never actually met a black person.
Cid Highwind, while not quite as bad as some of the other characters in the film, nonetheless slips into the valley due to his overly stiff cheek and eyebrow muscles that dont seem to gesticulate properly◊.
Rude manages to avoid this trope somewhat, but this is due almost entirely to his eyes being hidden behind his sunglasses for the majority of his screen time. And surely enough, the few shots in which his eyes are visible plunge him straightinto the valley. The fact that his bald head, chin and facial hair look almost like smooth plastic does not help matters.
Averted and then played straight with Aerith, who went through several changes during the production process as the designer (likely in some recognition of this trope) tried to make her as cute as possible. She turned out alright when her face◊ was finally revealed towards the end of the film. For the Complete version however, they chose to update her skin and eyes with sharper graphics which if anything just makes her look weirder. They even had to remove the original end-credits scene of Aerith (in spirit form) hovering over Cloud's shoulder, since it looked too creepy otherwise.
Ironically, it is the characters who are supposed to be inhuman who end up looking the most natural:
Kadaj◊ and Sephiroth◊ have green, cat-like eyes, but this somehow adds more soulfulness to their facial expressions, making them feel more lifelike and less like hollow-eyed puppets. This is especially notable in Sephiroth's case, since he rarely blinks and, according to the animators, doesn't even breathe.
The same goes for Vincent, whose overt stylization consisting of deep red eyes and pale skin◊ consistently reminds viewers that he is not human, thus making him look cooler and less like a human with something gone horribly wrong.
Of all the human characters, only two manage to avoid falling victim to this trope—for the most part:
Clipboard has a very disturbing walk, very disturbing facial expressions, and very disturbing everything else. Sure, there is a plot twist in that Clipboard turns out to be a robot, but it's still creepy.
Most of the human characters in the store look creepy as well, especially the woman and her baby.
The characters have an issue with unnatural body movements and dead-looking, glassy eyes. Both are actually due to the film being reworked on a shoestring budget after the original files were stolen. The initial trailer shows none of the awkward movements or creepy stares.
Mars Needs Moms is all over this. After all, Robert Zemeckis is involved with this one. Quite a few websites have noted that the humans look a lot more creepy than the aliens.
Monster House, while being motion capture, avoids making the characters look unintentionally creepy via Stylistic Suck that makes the textures more plastic looking as well as having a disproportioned, cartoony character design. What can come off as off-putting are the movements of the characters being too fluid and realistic. Of course, it's technically a horror film for children, so any creepiness suits it.
Usually the ones quoted for this trope are the Halloween Town citizens, but a lot of fans think the elves are creepier, mainly because they're too cheerful. And the human children are creepier than most things hanging around Halloween Town, anyway.
Jack and Sally crossover Fan Art drawn realistically has Sally usually look okay, but there's a reason why Jack is acartoonyskeleton.
Blue Sky's film adaptation of The Peanuts Movie can be unnerving to some. The CGI animation is a little too good at mimicking the art style used in the comic and specials, making everything look like so many colored balloons glued together. There's the fact that they gave the characters realistic hair and skin textures, which can be jarring, and everyone keeps the little dot Black Bead Eyes they had in the comics, making them look like black-eyed porcelain dolls. Snoopy in the trailer can be particularly unsettling due to having realistic fur and a real leather dog collar which doesn't sit very well with his exaggerated cartoony shape and design. Not only that, but the movement very closely mimics the choppy, rough movement in the original cartoon specials, which can be quite off-putting to a lot of viewers.
The Polar Express, although more successful, is notorious for this trope. Many reviewers commented on the zombie-like appearance of the adult cast. Especially the ones voiced by Tom Hanks. The Cartoon Brew blog nailed it: "This holiday season, give your family nightmares!"
Rango: Beans in general. Rather than resembling a real desert iguana, she looks like a cross between a little girl's doll, an alien, and something almost equine. It's the lizard variant of Uncanny Valley.
Leon's face changes throughout all three movies. In Degeneration he visually looks like his RE4 version, but his face◊ however looks notably different from the other characters, also unlike in the games Leon is pretty stone faced and barely makes expression, thus he stands out like a sore thumb. In Damnation Leon's face looks much better, its still weird enough that it takes some getting used to, while the other characters look more natural. In Vendetta Leon looks the best of the whole trilogy except for some shots◊.
The animation itself deliberately has this, as it's CG-animated but much of the movie is animated on twos with no in-betweens (rather than most CG movies, which have more naturalistic animation with tweening and motion blur). The end result is that the film closely resembles traditional animation or, indeed, a comic book, giving it a very distinct look from most other films. Reactions tend to vary depending on the viewer, but the vast majority have praised the film's unique style, so it's safe to say that the negative aspects were averted.
This is also invoked with the three non-standard Spider-People. Spider-Ham is a Toon who uses Toon Physics in a realistic world, Peni Parker is an Anime schoolgirl who has deliberately Limited Animation, and Spider-Man Noir is a permanently black-and-white character who's always given heavy shading even in broad daylight. All of these characters are individually appealing, but put them alongside more traditionally CG characters and the result is pretty damn uncanny◊—intentionally so, to enforce the idea that they don't belong in this universe.
Not in the film itself, but the music video for Squeeze Me features Sponge-ified versions of N.E.R.D. mixing cutout photos and 2D animation. The result is... unsettling.
The very detailed images of SpongeBob and Plankton in the time travel parts have a bit of an uncanny vibe to them, in the midst of an already weird sequence.
Sandy's superhero form is that of a realistic squirrel. Not so bad on the show (where it's either a still image or a puppet), but here...
Strange Magic: The faces are detailed and expressive but still somewhat cartoony, meaning some of the expressions look off.
BKN Animation's 2008 film What's the Matter With the Hatter? seems like your average cheap mid-to-late 2000s direct-to-video children's CGI movie. Then you realize that almost everything is cel-shaded. Alice stares at you with wide, soulless eyes, her mouth movements are erratic, and the Cheshire Cat...!!