Bird features Charnel, a woman who has been radically altered by a wetware Tinker into some kind of bio-mechanical doll-person. She is also stated by the author to be an expy of the Plain Doll, so this makes a lot of sense. Charnel herself is fairly pleasant and benign, though unsettling at first.
In With Strings Attached, Brox looks and acts like a normal little child—until he/she starts acting his/her real age. Her/his whole mien shifts, which creeps out the four considerably.
In The Keys Stand Alone: The Soft World, Paul's eyes turn golden after he's hit by lightning, which weirds Ringo out “because he looked so goddamned inhuman.”
Advice and Trust: When Ritsuko ups Rei's emotion-dampener medication in chapter 8, Rei crosses the limit between "emotionless girl" and "creepy person who doesn't seem quite human":
If Doctor Akagi had been watching, she might of noticed the careful rigidity that Rei held her face to melt swiftly into a far more eerie stillness.
Nebiros in New Dawn is already an outlandish looking demonic clown, barely even human looking, so it might count as an aversion, as he does not look human enough to qualify for the trope. However, it is played straight with his speaking patterns. He talks as a whole like a young teenager, has no sense of personal space, views reality as a game and is oh so enthusiastic in a very child-like way about what he does. And, suffice to say, he does not see anything wrong with being a serial killer: "Because its so fun, watching em flail about like a fishy!"
In X-Men fanfic Mutatis Mutandis, Northstar is basically described as vampirically beautiful. Rogue notices when she stares at Northstar's face for more than a few minutes, he looks so eerily perfect that he seems creepy and surreal.
Kristoff: They're absolutely creepy. Kai: No, they're not. Kristoff: You're saying that only because you're a hopeless horseman and these are some automatons. Kai: Maybe. But I do like that they'll never kick me, or throw me off, or trample me, or generally act like jerks towards me…
In Through A Diamond Sky, Jordan takes the doppelganger issue mostly in stride...but is never entirely sure what to make of her husband's double, Clu.
The same author has Tron: Invasion (a very loose adaptation of TRON 2.0), where Jet and Mercury appear as this to each other. Jet observes that Mercury's face is a little too angular and her movements a little too precise to be human, while Mercury is vaguely put off by Jet's hair color, the lack of circuitry under his gridsuit, and the "strangely flat" quality to his voice.
In Morphic, this comes into effect in Chapter 13 after Jean accidentally "evolves," causing her face and limbs to get out of proportion. The trope title is even stated word for word.
Loopers caught up in The Infinite Loops will sometimes muse on how non-looping individuals and even nonawake versions of looping individuals are disturbingly static and predictable. On the flip side, young loopers or particularly competent nonloopers will sometimes view Loopers as strange eldritch forces inhabiting the bodies of their friends.
In The Conversion Bureau: Not Alone and its sequel The Conversion Bureau: Conquer the Stars, the newfoals are able to get sad, scared and even annoyed and frustrated, but they can't get angry or assert themselves. The natural born ponies are revealed to be unsettled by this, while the humans are just put off by how the newfoals possess their former human selves' memories and none of their original personality.
To a lesser extent, Comet Tail in the Asia Side Story finds regular earth horses to be rather unsettling and strange looking, though she notes they are still just somewhat better than the Newfoals. Another character named Sergei references this trope by name.
Thousand Shinji: Asuka's secondary form is frightening because she looks like a demon... and her skin and hair's colors don't look natural on a human.
My red skin. As in brilliant crimson, the colour of arterial blood flowing from a fresh wound, before clotting has kicked in. It was the sort of colour more associated with paints than with the spectrum of human flesh tones. It was unnatural and terrifying with its ultimate wrongness for it had not the same quality as painted skin either. The same went for my hair. While copper was an accepted hair colour, mine was bronze. Again, it wasn’t so much the colour in of itself that was wrong, it was the fact that it was on a human, because it didn’t look like some strange admixture of blonde and red that might arise in nature, but it looked like it was made out of actual strands of metal. It just subtly did not look right.
Deserted Distractions: After confronting the shadow demon, Yami Bakura's hold on his "human form" slips, and Tea has this reaction to him.
This being was still human-shaped, still had the pale skin, brown eyes, and dead-white hair of the boy standing next to her[...]but he looked almost...stretched. Too tall and not wide enough, like a badly enlarged photo. His fingers were too long and too much like claws. His skin didn't seem to be quite opaque. If she looked hard, Tea could see the guttering shadows through the outline of his form.
Harry Potter is creeped out by conjured items in Barefoot because of his ability to read the history of anything he touches. Conjured items only have a history of minutes or hours and it weirds him out, especially since he can often tell the history of something from before it was made (such as how old a tree was when it's wood was used to make a wand).
Everyone finds Kaworu unsettling in Neon Metathesis Evangelion, whether it's his odd manner of speaking, unusual conversation topics, or constant smile. Furthermore, Maya is highly unnerved that in Sync tests his sync ratio never moves at all, something she finds completely inhuman as it would mean he's always focusing on the task to the exact same degree with the exact same success.