In Spirited Away, the spirits seem to have this opinion of humans, or at least of Chihiro Sen. Likely because, despite many taking humanoid forms, they're not actually human spirits, but creatures like weasels, etc.. Furthermore, most the spirits react to Sens odor, being able to tell she's there by her scent and not finding it pleasant.
In a filler episode of Dragon Ball Z, Vegeta and Nappa (who are Saiyans) land on a planet inhabited by bug people. They are arrested and thrown into a dungeon. Some of the prisoners remark on how hideous the two are to them. One of the more sympathetic prisoners calls his companions out and says it doesn't matter what they look like.
In Miracleman, Miraclewoman gets this from the most advanced being in the universe, a brain the size of a continent. "In spite of your ugliness, you are wise."
In Zits, a fly declares Jeremy ugly just as he declares the fly ugly.
Blind Green Lantern Rot Lop Fan, who himself looks a bit like a cave salamander, was kind enough to sympathize to fellow Green Lantern Katma Tui on how hideous she felt to him, despite her lovely voice. While Katma isn't human exactly, she does looks human (albeit with pink skin).
A story of Brazilian comic Bubbly (Astronauta) had the title character being called to investigate a fraud on an alien beauty pageant. Bubbly teams up with a Starfish Alien who thinks that Bubbly himself is hideous. They arrive at the planet, where another ugly alien dislikes Bubbly's appearance. Then comes the pageant, and every contestant is only pretty for the aliens◊ (the winner gets Bubbly into bouts of nausea, before they discover she was the fraud).
Bast, the Egyptian Goddess of Cats doesn't exactly say Morpheus is ugly, but in The Sandman issue "Season of Mists", she says she finds him much more attractive in cat form. Bast is an anthropomorphic cat.
In Earthsong, one of the characters is a spider-like being. Others are a little unnerved by his appearance, but he reveals he finds them just as unnerving. Specifically, his race is telepathic, and uses their mouth only to eat, which they consider a private thing. Therefore, he is repulsed whenever he sees normal people talking with their mouths. Seen here.
Superman once got into a Let's You and Him Fight situation with Pax Galactica, a team of intergalactic warriors. Eventually, their leader Lourdes agrees with Superman's suggestion to stop fighting and team up against the true enemy. One of her teammates complains, saying Superman is too ugly to stand being near.
Films — Live Action
In the original Planet of the Apes, Dr. Zira has to get over her human revulsion when Taylor asks for a goodbye kiss. She also remarks how ugly he looks after shaving off his beard.
Star Trek: Generations: The first thing the Duras sisters see through LaForge's VISOR is Dr. Crusher. Their response? "Human females are so repulsive!"
Halloweentown III: Halloweentown High has the main character's brother falling for a troll. At the end, they are about to share a kiss, but they both say that it is too weird/gross, and decide to stay as friends.
Davidge:(after Jerry saves Davidge from sand monster) You saved my life. Why? Jerry: Maybe I need to look at another face... even one as ugly as yours. Davidge: So you still think humans are ugly? Jerry: Compared to a Drac? VERY ugly. But that thing out there... is even more ugly than you. Davidge:(sarcastic) Thank you. Jerry:(grinning) You... are... welcome.
In Alan Dean Foster's Nor Crystal Tears, the Thranx are deeply unnerved and revolted by humanity's endoskeletal bodies and bizarre upright posture. Of course, humans return the favor, as Thranx are essentially four-foot-tall praying mantises. Fortunately, both sides largely get over those gut reactions with a lot of work. Played with a bit also, as many thranx find humans' flexibility remarkably graceful, even if they're ugly otherwise. Likewise, even the most insect-phobic of humans have to admit that thranx smell lovely.
In The Cyberiad (a short story collection) robots see humans (whom they call "palefaces") as the most disgusting creatures in the universe.
One of Ijon Tichy's voyages in The Star Diaries has him dealing with a United Nations-like federation of aliens. He finds their appearances bewildering (initially thinking his sponsor for Earth's admission into the group is a vending machine)—and the aliens find humans revolting on a molecular level (levorotary amino acids?! Disgusting!).
In The Amber Spyglass, Mary Malone stays with a village of mulefa, wheeled antelope/elephant-like creatures. They're intelligent and kindly and adopt her readily — but they admit, even after months of getting to know her, that they find her shape ugly and hideous because she's utterly unlike anything they've ever seen.
In Stephen King's short story I Am the Doorway (appears in the collection Night Shift), aliens infect an astronaut, and eyes appear on his fingers. Those eyes see everything in the world — but especially humans — as monstrous and abominable.
In the novel Transformers: The Veiled Threat, the Decepticons wax at length about how ugly they find humans. Even an Autobot comments to a swimming human ally that he likes her better when she wears her goggles, as they give her head a more robotic look. Of course, they are giant, mechanoid, robotic aliens, so their perspective on what is attractive is very different to say the least.
In Le jour des fourmis (i.e. Empire of the Ants), Arthur Ramirez uses a small TV screen in order to show the human world to the ant 103th. Afther seeing some models, the soldier ant said in her head that she find the human females very ugly!
In the Worldwar novels, the aliens refer to the humans as big uglies, which is somewhat ruder than us calling them lizards.
Variant: While the Auditors of Discworld have no concept of beauty or ugliness, they find the human form repugnant due to its possession of (Ewwww!) orifices, with all the messiness and inefficiency such features entail.
In Planet of the Apes the novel, the human protagonist Ulysse and female ape scientist Zira feel mutual intellectual attraction. Once they Almost Kiss... but Zira can't bring herself to it, as Ulysse is too ugly in her eyes.
In Charles Pellegrino and George Zebrowski's The Killing Star, the alien who captures Hollis and Wayville is struck by how ugly they seem to him.
In Fate of the Jedi, Luke Skywalker tells his son Ben that it's okay to think that the Kel Dor are ugly, because it's all a matter of perspective.
Luke: "Tell you what, if you think it's wrong for you to think of them as ugly, just think of how you look to them. Short, squat, unlined skin, a nose that puffs up like a rodent, tiny little mouth with jagged white things in it, a horrible shrub-like growth on your head."
Ben: "This, from the man who's worn a bowl-cut hairstyle almost all his adult life."
In one of the Star Trek: The Lost Era novels, a Romulan reflects on how humans look horribly unfinished to Romulan eyes; as if their ears and brows were only half-formed. Another book in the series suggests that to those humanoid races with ridged foreheads or brows, humans actually look infantile, reflecting a "typical" humanoid baby (the young having less pronounced ridges). Among the human-like races, humans are thus bland and disturbingly undistinguished.
The conquering aliens in the Pandora's Planet series of short stories (later anthologized under that title) seek to play up this trope after capturing Earth, to limit pro-human empathy by members of the alien race.
In the novelizations of the Alien vs. Predator world, when the point of view is from a Predator, if they are looking at a "ooman," they refer to him/her as "ugly," "pale," or "sickly."
Terry Bisson's short story "They're Made Out of Meat" has a race of energy beings that find us, but choose not to talk to us because our meatiness squicks them out.
In Animorphs, resident alien Aximili eventually figures out that humans use clothing to cover those parts of their body which they find ugly or socially offensive. He's convinced they cover all the wrong parts, though, as no human ever seems to think to wear something over their ''hideous nose'!'
In Chess With A Dragon, humans are one of only a dozen mammalian races in a galaxy dominated by thousands of reptilian and invertebrate civilizations. The only races that don't think we're unspeakably disgusting are the ones that think mammals like us belong on a plate.
The Stainless Steel Rat Saves the Universe has humanity involved in a genocidal war with slimy tentacled aliens, simply because they find us so repulsive. The protagonist discovers that the Grey Men (villains from a previous novel) are using brainwashing to engineer the war, and so he uses the same technology to make the aliens see the positive aspects of humanity. Like our slimy sweat and flickering red tongues.
Blair: You are displaying the childish human weakness of hating the different. On its own world it would probably class you as a fish-belly, white monstrosity with an insufficient number of eyes and a fungoid body pale and bloated with gas. Just because its nature is different, you haven't any right to say it's necessarily evil.
In C. S. Lewis's Out of the Silent Planet, Ransom is watching some tall, lithe, majestic Sorns walk toward him, and notices some very odd, short, chunky creatures walking alongside them with a gait that looked like piledrivers. He then realizes that the odd creatures were humans like himself, and that he'd spent so much time on Malacandra that he was now looking at humans with alien eyes.
In the Myth Adventures short story "Myth Congeniality", the drop-dead-gorgeous Bunny is rated lowest in a cross-dimensional beauty contest, competing against females from hundreds of nonhuman and non-humanoid species. But she wins the prize anyway, being the only contestant who wasn't disqualified for cheating.
In The Mirrorworld Series most Goyl are repulsed by the softness of human flesh, even Will, who gradually becomes disgusted by Clara. Kami'en is a rare subversion, the first Goyl to take a human wife. Other inter-breeding is mentioned in passing, though, suggesting that he's not the only one with an attraction to humans.
Live Action TV
Star Trek: The Next Generation, "Home Soil": The ship is taken over by intelligent microscopic crystals that call humans (and every other sentient being on the Enterprise) "UGLY BAGS OF MOSTLY WATER".
The Ferengi tend to find humans (and human-looking aliens) repulsive, and think those members who believe otherwise to be deviants.
(Lwaxana Troi and Deanna Troi have been captured and stripped naked) Deanna: Why have you removed our clothing? Guard: Females do not deserve the honor of clothing. Lwaxana: They're as bad as humans. Look at that leer on his face. Daimon Tog: Actually, his is a look of revulsion. But it is not a feeling that I share. (stares at them pervertedly)
In Angel, the demon residents of Pylea consider humans repulsive. The Groosalugg is respected for his warrior prowess but shunned for his human-like looks (he's Mr. Fanservice by our standards, Lorne describes him as the lovechild of Fabio and Keanu Reeves).
The Groosalugg: (confused that Cordelia finds him attractive) Don't you see this strange bulge in my arms? (points to his biceps) This strange curve in my mouth? (points to his mouth) My heart... beating in the wrong place? (puts Cordelia's hand over his heart on his bare chest)
In the prehistoric era of Chrono Trigger, the reptites (humanoid lizard beings) always call the humans "those hairless apes".
HK-47, the Ensemble Dark Horse (and sociopathic droid) of Knights of the Old Republic calls humans "meatbags" and wonders how they can stand to walk around as sloshing bags of organs. He can even cause the player character to feel a moment of self-doubt.
Mass Effect 2 has Garrus (a turian - humanoid equivalent of the link between birds and dinosaurs) as a romance option for a female Shepard. The relationship is based on inter-species If It's You, It's Okay - "I'm not going to pretend I've got a fetish for humans, but this isn't about that. This is about us."
The VUX from Star Control II are an entire race that think humans are so ugly and repulsive that they can't help but want them exterminated. Ironically, when the game starts, humanity thinks they're on bad terms with the VUX because, on first contact, the human captain involved insulted their looks, not knowing how advanced VUX Translator Microbes are. The VUX use this insult as the main reason for hating humans in order to cover up their bigotry, but you can pry the real reason out of them by asking repeatedly. Except for Admiral ZEX, of course...he finds them rather attractive...Hence his exile to an uninhabited world (except for his *ahem* menagerie).
Or remember the dialog when you first find a Spathi ship and you haven't allied with them yet.
In Warcraft III, in the first orc mission, when encountering the quillboars in Kalimdor for the first time, one of the orcs commented on the curiosity of the new beings with, "At least they're prettier than the humans".
In similar fashion to HK-47 Shale, the golem companion in Dragon Age: Origins, refers to all creatures of flesh, especially humans, as "squishy", "weak" and "disgusting" (the last mostly in terms of bodily functions). The only companion Shale respects almost from the very start is Sten, who isn't human, but a member of a race of large, strong and very durable humanoids.
Oghren, the drunken dwarf party member, also seems to find non-dwarven women (especially elven women, as he mentions to Velanna in Awakening) too thin and bony. At one point he may even call the Player Character ugly, while everyone else in the game praises their beauty. Doesn't stop him from shamelessly propositioning every woman he comes across though.
In Tales of the Questor, Quentyn reacts to his new sidekick's, Sam, demands to respect her modesty when she is forced to bathe by him by noting that he finds nothing attractive in beings like Humans and Elves who look like naked rodents to him. However, when Sam emerges, Quentyn notes that her now clean bright blonde hair looks nice, and that if she had proper body fur someone could come after her for her pelt.
"What is a tiny bit of extra pink in a sea of fleshy human disgustingness?"
In the Darkwing Duck episode "Twitching Channels", he and Megavolt are transported into our world and shrieks in terror at the "beakless mutants".
The animated Earthworm Jim series revealed that Princess Whats-Her-Name was actually the sister of the Big Bad, the hideous Queen Pulsating, Bloated, Festering, Sweaty, Pus-Filled, Malformed Slug-For-A-Butt. However, the Princess was born horribly deformed, with a slender body, pink skin, long red hair, and large eyes. Yeah, that's right: Everything that makes her an over-the-top cartoon hottie to humans makes her hideous to Insectikans.
On the Gargoyles episode "The Mirror", Goliath mentions that he never realized Elisa was beautiful until she was turned into a gargoyle. She replies "You mean you thought I was ugly?" Goliath quickly changes the subject.
This is Granamyr the Dragon King's opinion of humans in He-Man and the Masters of the Universe (1983). In one episode, a fellow dragon named Tor and a human girl named Lyra fall in love. Tor describes his sweetheart as "the loveliest and sweetest being I have ever known". Granamyr is baffled.
In the Spongebob Squarepants episode "Band Geeks", Squidward's band ends up playing at a human football game.
Patrick: These are some ugly looking fish.
Spongebob: Maybe we're near one of those toxic waste dumps.
Mr. Krabs: I think I'm gonna be sick...
What the bugs from Thumbelina think of the title character after she's accidentally stripped of her bug disguise.
In Ben 10: Omniverse, Rook reassures Kevin that he won't hit on Gwen by claiming that "Gwen is only attractive by human standards". To Gwen's chagrin, Ben confirms Rook's opinion saying there's "no comparison" between Gwen and the females of Rook's species. Gwen's patience runs out when Kevin then quips "so to him Gwen would be like an orangutan wearing glasses?" and she launches Kevin and Ben out of the ship.
Deconstructed by humanity's attitude to earthbound "alien" species, like cuttle fish, or trees. No one... sorry. Almost no one would view them as sexy, but most think forest pictures are relaxing, and the exotics fascinating. And then there are the faster cars and aircraft... there is beauty in good design. Which is one of the places where our fascination with nature and science comes from. It doesn't make much sense to assume that any technologically advanced species could evolve without this trait.
Otherkin, Therians, Na'vi-kin and other people with body identity disorders who believe themselves to belong to species other than the human race tend toward this. It's played for laughs in public, but...