Played with in A Brother's Price. There are the Whistlers, the hero's family, who are all very good-looking. Their neighbours, the Brindles, "look like horses" according to Jerin, and have a reputation for starting fights at markets and fairs and the like. Then there is Keifer Porter, who allegedly was very, very, pretty, but also very, very cruel towards his wives, using psychological abuse against the older ones, while physically hurting at least one of the defenseless, younger ones.
In Jaqueline Carey's Kushiel's Legacy, we are sympathetic (politically) towards the D'Angeline people, who are all beautiful. That is not to say that there aren't D'Angeline villains, and non-D'Angeline heroes, but for the most part, this fits into the trope. More often than not, Non-D'Angeline characters of importance are either attractive or 'skilled' enough for their heritage to not matter.
In all this ancient and mysterious history, the most mysterious figures of all were without a doubt the Great Circling poets of Arium. These Circling Poets used to live in remote mountain passes where they would lie in wait for small bands of unwary travelers, circle around them, and throw rocks at them.
And when the travelers cried out, saying why didn't they go away and get on with writing some poems instead of pestering people with all this rock-throwing business, they would suddenly stop, and then break into one of the seven hundred and ninety-four great Song Cycles of Vassillian. These songs were all of extraordinary beauty, and more extraordinary length, and all fell into exactly the same pattern.
The first part of each song would tell how there once went forth from the City of Vassillian a party of five sage princes with four horses. The princes, who are of course brave, noble and wise, travel widely in distant lands, fight giant ogres, pursue exotic philosophies, take tea with weird gods and rescue beautiful monsters from ravening princesses before finally announcing that they have achieved enlightenment and that their wanderings are therefore accomplished.
The second, and much longer, part of each song would then tell of all their bickerings about which one of them is going to have to walk back.
In the Earth's Children series by Jean Auel, Ayla is this by Cro-Magnon standards (she's muscular, blonde, and blue-eyed), but she spends the first book, Clan of the Cave Bear, adopted by a Neanderthal family with different standards of beauty, and so grows up thinking that she's ugly. It isn't until the second book, after she is exiled from her clan, that she runs into someone who looks like her and treats her as if she's beautiful.
Played almost laughably straight with Hester Prynne of The Scarlet Letter, whose beauty the narrator goes into ridiculous amounts of detail describing. On the opposite side, her neglectful and vengeful husband has mildly deformed shoulders and becomes more malevolent-looking as the book goes on. A bit of a subversion exists, though, in that the main narrative thrust of the book centers around the fact that Hester is a sinner and an adulteress, and how she suffers for her actions; it's somewhat debatable as to just how much sympathy Nathaniel Hawthorne has for his character. This applies even more straightly to Hester's daughter (who is even named Pearl), though, as among other things Hawthorne drives home the fact (with a piledriver) that the sins of the parents do not apply to the innocent children. And in the mid-19th century, some people really needed to be told that, to be honest.
In J. R. R. Tolkien's Middle-earth world, this trope shows up most prominently with the Elves and the Orcs. The Elves are especially fair while the Orcs are especially ugly. In their case, Elves are created to be especially fair among the children of Ilúvatar - "elven-fair" is a descriptor indicating great beauty. The Orcs are ugly due to the malicious corruption of the first Dark Lord Morgoth - they came into being through his twisting and corrupting of Elves. For Men, heroes like Aragorn and Túrin follow this trope, their looks even being compared to those of Elves. Hobbits and Dwarves tend to be plain looking, if not ugly - but Frodo is fairer than most other hobbits.
On the other hand, the trope is also subverted through elements like the Druédain or Wild Men, who are ugly compared to other Men but firmly aligned with good. They remain so for thousands of years while most of the Númenoreans, the most Elf-like of Men (specifically blessed by Ilúvatar to be so) are corrupted by Sauron - who himself had a fair physical form before the events of The Lord of the Rings. While Frodo may follow this trope, Sam is not especially handsome. Hobbits generally look "good-natured rather than beautiful".
An example who was once a subversion: To the vast surprise of most people, Lancelot in Le Morte d'Arthur and other early Arthurian works is not the handsome "Prince Charming" figure he tends to be portrayed as in modern media, but a stocky, barrel-chested walking meat wall who is notably plain in appearance. (He's also a mentally unstable berserker given to complete psychotic breakdowns at the drop of a hat. Naturally, since John Cleese is an Arthurian scholar, Monty Python and the Holy Grail got him completely right.)
T.H. White takes this even further in The Ill-Made Knight, the third volume of The Once and Future King, and makes his version of Lancelot extraordinarily ugly, so much so that he is said to resemble an ape.
Further subverted The Once and Future King series with Elaine. She starts off as being young and beautiful, but becomes plump and reclusive from society when Lancelot abandons her. The narrator even mentions that she did the "wrong thing", and ought to have turned "thin and interesting" as Guenevere would have done in that situation. Elaine is still portrayed very sympathetically (even if she does trick Lancelot into sleeping with heragain)
Bernard Cornwell's The Warlord Chronicles retained the good-looking "Prince Charming" Lancelot and then thoroughly subverted it, turning him into a cowardly, snivelling, petulant bastard with no redeeming features whatsoever. He didn't even have the good grace to be magnificent about it. One could argue in fact that Lancelot is the major villain of the series- he's certainly one of the least likable characters.
The series Twilight is especially notorious for this trope, seeing as Bella's narration does nothing but describe other characters' physical appearances and how wonderful or horrible it makes them as a being, depending on how they look. She primarily judges people based on their looks, so you can tell how important and "nice" a character's going to be based on how Bella finds them attractive. The only exception to this rule is Rosalie, who's depicted as shallow and vain, but that's just Meyer expressing her blonde-female hate.
As an even more subtle example, James (the Big Bad of the first book) is described more than once as extremely plain, as compared to the Cullens' inhuman beauty. The reason? Meyer has said that he was a total gonk as a human, and only the powerful beautifying nature of vampirism turned him barely average. On the flipside, all the Cullens (the good guys) were already gorgeous before they were turned, and just got hotter as vamps.
Bella never gets over her prejudice for looks. In Breaking Dawn, an Amazonian vampire vows to protect the Cullens against an invasion and offers to train Bella to fight and use her superpowers. Bella's response is to never feel comfortable around the woman because her "wild" looks "scared me to death". The Amazonians ultimately prove loyal, but Bella never apologizes or admits that she was wrong.
Bella's prejudice towards those she doesn't think are good-looking goes to such an extent that she treats those she doesn't find attractive with utter contempt, even if they're being friendly to her, but if a good-looking person does questionable things to her, she doesn't mind at all. She actually thinks that a person's physical beauty makes up for any of their flaws, and shows far more respect to the beautiful Cullens than to her own father. When Edward admits to watching her sleep every night, Bella thinks it's very sweet of him. If he was any less attractive, she would have had him arrested.
The only human person she considers "helpful" instead of "annoying" in the first book is Mike, who acts exactly like everyone else except he's the cute jock versus the eccentric and the nerd. Even when dismissively comparing him to a dog, Bella still thinks that Mike is "easy to like" and attractive, while Eric is "oily" and "overly-helpful" and Tyler merits no special attention at all, except to say that he's irritating (he nearly killed Bella once, when he lost control of his truck, and desperately wants to make amends to her; but Bella dismisses him as a nuisance).
Also Lauren, who is nasty to Bella out of pure jealousy and described as having "fishy" eyes and a "nasal" voice. Or when Bella first sees Bree the newborn vampire and her first thought is to determine if Bree is attractive or not. It's not limited to Bella either - the final chapter of Eclipse that is told from Jacob's point of view has him reflecting that he once thought Leah was attractive but now he finds her repulsive ever since she got all upset over Sam dumping her for Emily.
Tellingly, Lauren is only described unflatteringly after she makes it clear she dislikes Bella - the description of her voice as "nasal" takes place while she's mocking Bella, and most of the negative comments about her appearance are during a passive-aggressive verbal spar the two are having.
It is made clear that Edward is gorgeous-looking very early in the book. It is also made clear that he's perfect: irresistible voice, super senses, many supernatural abilities, etc. Stephenie Meyer describes his dazzling beauty and perfection to the reader over and over again until it feels like listening to Kaepora Gaebora.
In Jane Austen's Pride and Prejudice the first thing characters note about one another is how physically attractive a person is. Considering the original title of the book was First Impressions...
Jane Bennet, who is considered to be the most beautiful women in the neighborhood, has a 'good' personality, such as being sweet, kind, patient, and understanding and always sees the best in people.
This turns out to be the case with Astrid in Eight Days of Luke, who's described as "quite pretty" from the outset even while she's being lumped in with protagonist David's other uncaring relatives. As the plot unfolds, Astrid comes to realize how poorly she's treated David, and she eventually becomes his loving guardian and friend, while their unattractive relatives are revealed to be outright evil.
The Phantom of the Opera. The adaptations have various takes on Erik's deformity. He still is evil, though. Though it's made explicitly clear that he became evil and insane because people shunned him for his appearance, instead of appreciating him for his considerable genius. Erik originally became evil because, with his deformity, people assumed this trope, and...well, it's very hard to turn out goodif everybody insists you're evil from the moment you're born.
This trope is believed by the fairies in Jonathan Strange & Mr Norrell, and the person he's specifically applying it to is indeed good. But otherwise the trope isn't particularly in play.
Partly lampshaded, partly averted in The Man Of Feeling by Henry Mackenzie, where many times, instead of giving the reader a physical description of characters, Mackenzie simply has the main character Harley employ his knowledge of "physiognomy" (the science of determining personality by someone's appearance), and goes straight for the moral judgement.
When Stevie Rae died and then un-died, she was repulsive and smelt really bad. When the ritual to give her and the other Red Fledglings their humanity back was complete, they were all pretty again.
Also, the Bull of Light, which is black is described as "deep, mysterious and beautiful to behold," compared to the Bull of Darkness, which is white and is described as "a nightmare come alive."
Elliot is probably the only fledgling in the entire series who is not super gorgeous, being described as fat, pasty, freckled with nappy carrot red hair. He's also supposedly annoying, lazy, and stupid, and in his first appearance a teacher berates him for not being special and unique like every other male vampire, and this is never shown as a problem. When he starts coughing in class, a sign that everyone knows to mean death is imminent for a fledgling, all Zoey can think of is how he's being annoying and should ugh, just get a cough drop already! When he finally does die, all Zoey can say about him is that it's not sad that he died, it's sad that no one liked him. In his subsequent appearances as a Red Fledgling, Zoey doesn't even refer to him as a person like she does the others, instead referring to him as "That horrid Elliot creature."
Any old person of significance that is on the side of good, like Grandma Redbird or Mary Angela, are strangely bereft of wrinkles for people their age.
Kalona is stated to be a serial rapist demon god who will supposedly destroy the world, but Zoey thinks he can change. Why? Because he's the most beautiful guy ever. In Destined, Kalona pulls a HeelFace Turn.
The Raven Mockers are half human, half raven monstrosities, but Rephaim, when he falls in love with Stevie Rae and becomes good, its revealed he can become an extremely hot human if he wants.
The cats aren't even immune. Of course Zoey's cat Nala is cute and Likable, while Aphrodite's cat is horrible and mean, and the only cat described as being ugly in the books. She's named Maleficent if it isn't obvious already that she's horrible.
Zoey's stepdad, a Straw Fundamentalist religious fanatic is described as having thinning hair, Chicken legs and horrible fashion sense. He's portrayed as a cartoonishly closed minded bigot who berates anyone for the smallest of differences, cheats on his wife, and drinks beer even though he says he doesn't. Other women in the Peoples of Faith, the stereotypical religious fanatic group he's an elder for, are described as fat, balding and beady eyed with pedophile husbands.
Sisterhood Series by Fern Michaels: Played straight as an arrow! Check this out for proof. The bad guys are mostly ugly as sin to start with or beautiful in a fake way but become ugly by the end. Of course, Lizzie Fox's marriage with Cosmo Cricket cheerfully goes into Ugly Guy, Hot Wife territory.
A short story by Dick King-Smith might count as an inversion where the protagonist is a male fairy and is ridiculed by all the others except one who is described as "not very pretty but had a kind face". At the end when said fairy is kind to him he realises how beautiful she actually is, suggesting that maybe goodness equals beauty.
Played with all over the damn place in the Sword of Truth. The list of hot evil chicks and handsome evil dudes is about as long as their good counterparts. In fact, its implied that their good looks helped them on the road to be big enough bads to seriously break things.
At first she wondered if he could be a fugitive from justicethe perpetrator of some horrid crime, who dared not divulge his true name even in the remote fastness of a Bornean wilderness; but a glance at his frank and noble countenance drove every vestige of the traitorous thought from her mind. Her woman's intuition was sufficient guarantee of the nobility of his character.
Played straight and inverted in Inheritance Cycle. On the one hand, a lot of the protagonists are described as attractive, especially the elves. On the other hand, said elves can and do use magic to shape their own bodies. One character says something to the effect of every elf looking exactly like they want, and some are described as terrifying and animalistic. Not to mention that some of the elves, like Vanir, may be on the protagonist's side, but hardly embody "good".
In keeping with the interested study of good versus bad, competent versus incompetent, and the hilarious world of deadly political machinations, The Wheel of Time has the important characters as beautiful more often than good or evil per se. Some of the more attractive characters are important in part because of how they use their looks to get ahead, such as Berelain using her sexuality to help play the neighboring rulers off of each other.
Every single one of Danielle Steel's protagonists is stunningly gorgeous or handsome, without any extra effort or help needed, and if they're over forty, it's frequently mentioned that they look much younger than they are. The closest she's come to an unattractive heroine is the Hollywood Pudgy title character of the novel "Big Girl". The beauty is just the tip of the iceberg, as most of them border on Purity Sue—intelligent, hard-working, etc. Any "flaws" only serve to make them more endearing and appealing.
In "Prince Charming", this seems to be true of Vasilisa, though Prince Dmitriv and the other courtiers can hardly believe it. Only because they are cynical, though.
All of the protagonists of The Last Dragon Chronicles are described as - at the very least - good-looking at some point. Then, most bad guys are ugly as road kill. AND THEN you have everyone who got infected by the Shadow - horribly deformed. But they're back to being pretty after it's gone.
A noticeable trend throughout the Divergent series, all the good guys are described as pretty or beautiful. Averted with Peter, who is a complete jerk, but is repeatedly described as being good-looking.
Brazilian book O Fantástico Mistério de Feiurinha displays this thoroughly when telling Feiurinha's story. The main character gets her name from the fact that she was kidnapped by three ugly witches as a baby, and raised to believe she was the ugly one and the witches were beautiful. It's not until she witnesses her companion goat turn into a handsome prince, due to her unwittingly breaking a curse cast on him by the witches, that she discovers the opposite is true.
In Declan Finn's Honor At Stake, literally true with vampires, whose souls are more tightly bound to their bodies and have stronger effects than human's. Amanda is beautiful and avoids many limitations such as holy objects and invitations because she's not evil. (On the other hand, she's less powerful because she drinks less blood.)
In English literature, The Picture of Dorian Gray, is a deconstruction. Wilde was critiquing the commonly held belief during the 19th Century that physical appearance both reflected and was influenced by morality, piety, and social status. The trope still applies to the portrait of the protagonist and would have applied to him had he not sold his soul.
A strange example - neither subversion nor aversion but not completely straight either - comes from the work of Rex Stout. Stout wrote a short story called "Murder is No Joke" in late 1957. One of the characters, Flora Gallant, is a fat, shrewish, bitter, ugly, crude middle-aged female social misfit - virtually a perfect example of the trope played straight. The next year, Stout was asked by the Saturday Evening Post to expand the story into a novella. In this version, Flora Gallant is a gorgeous, vivacious young woman who romances Archie to some success - the opposite of the trope. The rest of the plot, including the identity of the killer, is identical, except that in the first story, Archie has Flora tagged as the killer; in the second, he thinks she's the next victim. She's neither.
Charlotte Brontë stated that she deliberately created Jane Eyre to be "as poor and plain as myself," in contrast to the beautiful and elegant romance heroines of her time. Consequently, Jane Eyre herself is never seen as anything but plain and unassuming, except in the eyes of her beloved - who in turn is not particularly handsome, but is loved by Jane for his sharp-pricked devotion to her. And, of course, the novel's prettiest characters are all extremely problematic in one way or the other. Blanche Ingram is a self-involved Gold Digger; Rosamond Oliver, while sweet, is nevertheless represented as a fluttery socialite-type; and St. John Rivers, although not a villain, is extremely manipulative and egotistical.
In "The Silmarillion" the Elf Prince (later Elf King) Fëanor is described as being quite good-looking, fitting in with his quality as The Ace among elves. However he is very arrogant, hot-blooded and obsessive, and comes across as a jerk, his actions, such as the kinslaying of the Teleri, leading to the Noldor being cursed for centuries.
Often subverted in Harry Potter.No matter how attractive the movie actors may be, characters are often described with more negative physical traits than positive—-for example Harry is introduced as having knobby knees, messy hair, and perpetually-broken glasses. Other evil characters, like Bellatrix Black and the teenage Voldemort, are attractive.
Bellatrix is sort of in between subverting and playing straight this trope - while she was clearly quite attractive, she is shown to be gaunt and worn from her time in Azkaban. On the other hand, the same is said about Sirius. And while Harry did think at one point that the Slytherins mostly appeared to be an unattractive lotnote it is likely this meant personality-wise, some, like Blaise Zabini, are considered to be quite attractive. Plus, seeing as Harry tended to be a bit biased against the Slytherins, there is a case of Unreliable Narrator to consider.
There are further aversions with the likes of Mad-eye Moody. Played straight with a few villains like the Carrows, and Millicent Bulstrode and Pansy Parkinson, the latter who is described as looking like "a pug".
It's also worth mentioning Gilderoy Lockheart. He's represented as very handsome and charming and has published several books about his various heroic deeds. It's then found out that he's been finding people who banish werewolves and such and modify their memory, then taking their credit. He claims that one reason he did this is that the people who did these things weren't very pretty.
The general rule is that ugliness will not make you become evil, but evilness will make you become ugly. Voldemort's looks began to deteriorate when he started using large amounts of dark magic resulting in his inhuman appearance, while Bellatrix lost her beauty through insanity and her stay in Azkaban. More morally ambiguous characters like the Malfoys are the middle ground; Lucius is never said to be particularly attractive in the books, and Draco is occasionally called ferret-like. Narcissa is beautiful because she's a Black (they're ''all'' described as good-looking, and later redeems the family through motherly love, however her beauty is marred by her snootiness.
Terry Pratchett's Discworld books take this entire concept, set it in the street, and kick it until it runs squealing. Consider how three of its major characters are usually drawn: Rincewind looks like an older Shaggy from Scooby-Doo; Sam Vimes resembles a cross between a craggier, unshaven Clint Eastwood and Pete Postlethwaite; and Granny Weatherwax, while blessed with excellent bone structure, is (by Word of God) a crabby old woman. Regardless of personal tastes, they're not exactly what you would call "universally attractive"... and they're also three of the main heroes of the Discworld (although Rincewind is not one by choice).
In Witches Abroad, the evil Lady Lilith (Granny Weatherwax's elder sister) is described as, essentially, looking like Granny would if she was a few years younger. This is partially an extension of Granny's subversion of the trope, and partly a straight-up Vain Sorceress.
On the other hand, a lot of younger female heroes are portrayed as quite attractive, especially love interests; look at Angua, Sacharissa, Susan, Adora Belle Dearheart, and Cohen the Barbarian's daughter Conina.
In the manner of middle ground, Moist von Lipwig, one of the more recent protagonists, is described as being utterly unmemorable, a trait he used to his advantage in his previous job... as a con man. Unmemorable to the extent that his own mother previously took the wrong child home from kindergarten, and he has to attract attention to himself while shaving.
Not that there aren't any good-looking heroes or unattractive villains on the Disc; for instance, Captain Carrot, The Cape, is as handsome as fits the character type (described by a female vampire as having godlike proportions—the better class of god, even), and Mr. Teatime, from Hogfather, is boyishly handsome but has one glass eye, and one "normal" eye that's even more disturbing. Sensibly, there's no easy way to tell alignment from appearance on the Disc. Not even if said appearance is standing on top of a massive pile of skulls... because said person might just happen to be Cohen the Barbarian.
Played straight and sarcastically lampshaded in Going Postal. A minor villain is described as being obese and looking like "a piglet having a bright idea", with a voice like "a small, breathless, neurotic but ridiculously expensive dog". He has exactly the personality one would stereotypically associate with these physical traits. In a footnote, the author notes that "it is wrong to judge by appearances" and that "snap judgements can be so unfair" but strongly suggests that such judgements are actually correct most of the time.
IN SHORT: Discworld averts (most of the time).
A Song of Ice and Fire both follows and subverts this trope with various characters. Many of The Beautiful Elite are admired for their regal or exotic appearance, such as Cersei Lannister or Joffrey Baratheon, but are actually quite incompetent and cruel. Others are mocked, belittled or hated for their ugly appearance, including Brienne of Tarth and Tyrion Lannister, but show far more compassion and integrity than many others. However, other characters follow this trope straight. Many heroic characters are described as being quite handsome or beautiful, such as Daenerys Targaryen (arguably) and Sansa Stark. Many villainous or anti-villainous characters are also quite hideous, such as Sandor Clegane (though he looks hideous due to his monstrous brother burning his face, leading to him becoming cynical and bad-tempered, though shows a kinder side occasionally, though it is very well-hidden). In general, a character's appearance is more likely to be an influence on their personality rather than a reflection of it.
A lot of the problems in the setting exist because the general populace believe this trope is true all of the time when it really isn't.
House Frey plays this straight — its darker members are obnoxious, scheming, backstabbers who are described as looking like weasels. There are, however, a few attractive Freys who are not as evil, most prominently Roslin Frey. Her oldest half-brother, Ser Stevron Frey, has his father's weasel look but is apparently amiable and good-natured, placing great importance on family.
Played very straight with Ramsay Snow (later legitimized to Ramsay Bolton). He is one of the most evil and unattractive characters in the series, described as being fleshy, with pink blotchy skin, thick lips, dark dry hair and sloping shoulders. Ramsay is an incredibly psychotic Sadist who is believed to have murdered his legitimate half-brother and has such a reputation as The Dreaded throughout the North that even his ruthless father Roose Bolton tells him to tone it down as it is making their House unpopular. Roose himself sounds very sinister, with a pale face that barely shows emotion or age, and icy blue eyes that are shared by his son. He ends up murdering his King to usurp control of the North.
Played with on Theon Greyjoy. When he first appears in the books he is quite an attractive character, but is an arrogant jerk, and ends up betraying Robb Stark when the Ironborn attack the North and even murders children. However, when he is captured by Ramsay Snow he is horrifically tortured, losing toes and fingers and ending up looking much older, with white brittle hair and pasty skin. He ends up becoming much more likable, even helping to save Jeyne Poole from Ramsay.
Similar to this, Jaime Lannister is very attractive but from early on in the books seems a clear villain and is one of the most hated men in the Seven Kingdoms for murdering the King he swore to protect. After he becomes more unattractive due to months in captivity and having his right hand cut off he reveals his reasons for killing the King, to prevent them burning down a city, and undergoes Character Development, becoming a much more sympathetic and likeable character.
Stannis and Renly Baratheon, Foils to each other. Renly is very attractive and charismatic, but is privately shown to be vain and greedy, planning to usurp rule basically out of arrogance and because he can gather a large army. His older brother Stannis is a rather scary-looking man, with a stern face, baldness, and who barely smiles. As the books continue, due to his blood being used for magical rituals by Melissandre, he becomes more gaunt and ages greatly. However, he is arguably one of the most honorable people in the series, always trying to uphold the law and stick to his morals, only claiming the Iron Throne because he believes its his duty to do so even though he doesn't want it.
Played straight with Janos Slynt, the slimy and incredibly corrupt commander of the City Watch, who is described as looking like a frog.
With Aerys II "The Mad King" he ended up looking terrible due to his insanity, becoming gaunt due to malnourishment out of fear of being poisoned, and not cutting his nails and hair due to fear of blades. As a result, even though he died at the age of 39 he had a terrifying appearance, with long unwashed, matted and tangled hair and beard and long yellow fingernails.
Sherlock Holmes was not described as terribly good-looking — and in fact his creator Conan Doyle criticized the stories' illustrators for their portrayals of the character, saying that he had always imagined Holmes as "uglier" than they had depicted him in their drawings (though he added that "perhaps from the point of view of my lady readers, it was as well"). Watson was supposed to be the attractive one (and quite a ladies' man to boot). Unsurprisingly, this is generally ignored in screen adaptations.
There is also an in-universe example: At the time of writing, this trope was considered universal truth, and Watson immediately fingers the ugliest suspect as the killer. Holmes merely tuts and points out that none of the killers he has put away was worse than average-looking, and that the ugliest man he has ever seen is a philanthropist who donates half a million pounds a year to charity.
Both played straight and subverted in Wild Cards, where most of the characters have hideous mutations. Most of the human-looking leads are not spectacular, either: the Turtle is a plain, chubby nerd; Fatman is, well, fat; and private detective Jay Ackroyd is good at blending in because he looks entirely average and nondescript. Golden Boy is handsome and has eternal youth to boot, but he's almost universally despised as a traitor (he didn't know the youth was eternal when he did it). Doctor Tachyon is handsome, as are his (mostly backstabbing) relatives, because Takisians are bred for beauty; thus, he often has trouble dealing with the less attractive Jokers because he was raised to believe that this trope was gospel truth. His psychotic grandson Blaise is described as the most attractive and evil character in the series.
Subverted wonderfully in Lois McMaster Bujold's Vorkosigan Saga, in which the main character, thanks to his mother being poisoned while pregnant with him, is a brittle-boned dwarf who is considered worse than unattractive by his mutation-horrified homeworld. Unsurprisingly, most of the women who look past that are 'galactics'; one of these is a genetically engineered prototype-soldier who's eight feet tall and as strong as two men. Eventually, even more subversive to this trope, Vorkosigan marries a woman from his own planet who loves him much more than her former, physically-attractive-but-a-total-jerk husband and thinks he's perfect the way he is.
In The Dresden Files, if a devastatingly beautiful person (usually a woman) shows up, chances are, he/she's bad news. Most common with vampires of the White Court, succubi and incubi; for the most part, they are by nature impeccably beautiful and normally evil, cold, evil, manipulative, and really evil. There are some notable exceptions, however: Thomas Raith, Harry Dresden's half-brother, is in a gray area, Karrin Murphy is described as being cute (though she's also a tough-as-nails cop), and Harry's early Intrepid Reporter girlfriend Susan Rodriguez was very pretty and a definite good person. The Faeries, and especially the High Sidhe, are also perfectly formed but run on Blue and Orange Morality.
Subverted in Graham McNeill's Warhammer 40,000Ultramarines novel Dead Sky Black Sun. Confronted with the Unfleshed — twisted, hideously malformed, with no skin on their bodies — Vaanes is horror-struck ("Look at them. They're evil"), but Uriel tells him he's not certain. He remembers the innocent children he saw herded to the process that transformed them, and sees that they have remembered the God-Emperor, erecting a huge statue of Him. Vaanes deserts him, but the Unfleshed are willing to support him in his quest. When most of them have died carrying it out, the handful of survivors need only be assured that the Emperor is pleased to be delighted.
Interestingly enough, this is in opposition to traditional Imperial dogma in the setting; creatures such as the Unfleshed would be seen as Chaos-tainted mutants and unworthy of acknowledgment as the Emperor's children- or indeed of basic human consideration as kindred.
In William King's Warhammer 40,000: Space Wolf novel Wolfblade, Ragnar reflects on how his Wolf Lord is the very image of a great hero, and his opponent in dispute is rather less preposing. Then, the opponent also had to be a great warrior and leader, to reach the same post as Berek — and while the opponent is arguing against Ragnar partly out of rivalry, by the same token, Berek is defending Ragnar partly from the same motive.
In Madeleine L'Engle's A Wrinkle in Time, they escape to the planet Ixchel where they encounter the faceless tentacled aliens, who look after and protect them. Indeed, one, in charge of Meg, is surprised by the terms she uses, such as "beast" to describe them, and Meg ends up referring to her as Aunt Beast.
Technically subverted in the Karavans series by Jennifer Roberson, as The Beautiful Elite are mostly evil. Everything ugly is evil too. Indeed, Always Chaotic Evil is rather a common species trait in these books...
The Doomsday Book by Connie Willis included as one of the heroes a villainous looking priest who is clearly presented as one of the finest people in the tale.
Voltaire famously penned a rather scathing poem, "Marquise", dedicated to a vain aristocrat who had spurned his advances because he was too old for her, despite being one of the smartest, wittiest guys of his time. The gist of the poem is "So I'm old and wrinkled. You will be too, sooner than you think". In a double subversion, Tristan Bernard later wrote a last stanza to the poem, his imagined answer from the Marquess : "But until then old man, I'm 26, and fuck you too". In those terms, because French poetry is hardcore.
Subverted, along with every other cliche of Space Opera, in Harry Harrison's Star Smashers of the Galaxy Rangers. Arriving on a new planet, our heroes see a war between the Garnishee (hideous tentacled monsters) and the humanoid Ormoloo (who don't look too bad if you overlook the four arms), so they wade in on the side of the more-or-less-humanoids. It's only after exterminating 99.9% of the Garnishee race that they discover that the octopoids are the wise, gentle and cultured good guys and the Ormoloo are the equivalent of cattle being mind-controlled by evil Puppeteer Parasite aliens out to conquer the galaxy.
In Meredith Anne Pierce's The Darkangel Trilogy, the titular angel (or vampire) is described as stunningly beautiful. He's also completely evil (securing his immortality by drinking the souls of young women), and the main character (who is described as average looking), falls in love with him, partly because of his beauty. The trope is played with however because the female protagonist knows that this is a terrible reason to love a person, and yet cannot bring herself to kill him. She eventually restores his humanity and in doing so he is said to lose some of his supernatural good-looks.
Another character in the story also claimed that the vampire is beautiful because he is not completely irredeemable; his soul was still there under all the evil, but when his soul was lost he would become hideously ugly.
Mostly averted in the How to Train Your Dragon series, where none of the characters are actually that pretty. The only exceptions to this would be Humungously Hotshot the Hero, and Alvin the Treacherous, who is steadily getting uglier with each book (most of it being consequences of his actions, mind).
In A. Merritt's classic novel The Moon Pool, The Big Bad is a beautiful being of light called the Shining One, who enslaves and vampirizes human souls. The lost race who worship it are classically handsome, but decadent and cruel. The forces of good, meanwhile, are represented by three decidedly weird-looking aliens and a race of frog-people.
In The Riftwar Cycle, beauty doesn't really equal anything. Villains are just as likely to be attractive as heroes (perhaps even more so), and most heroes are fairly unremarkable in their looks. Of the ones that stand apart, some are just ugly (Pradji with his squashed nose and pockmarks), others possibly attractive save for one or two off-putting qualities (Arutha's perpetual gloom, Erik's brutish face), and others are beautiful, but it doesn't do them any favors (Tomas's disturbing slightly-alien features, Sandreena's gorgeousness destroying her childhood). Similarly, all the elves of the series are beautiful, but you can't tell the good from the evil ones just at a glance.
On the other hand, the idea comes up: When Martin and Garrett run across a moredhel woman, the latter is surprised by her beauty, so the intrinsic expectation that evil enemies would look monstrous while good allied elves are the ones who are allowed to look beautiful is there.
The Gentleman With Thistle-Down Hair in Jonathan Strange & Mr Norrell explicitly considers handsomeness to be a sign of one's superiority and nobility over everyone else. A large factor in his decision to make Steven Black the King of England was his good looks. Since he's one of the worst of The Fair Folk this view is not particularly sensible, and it's not evident elsewhere in the books.
I might add that this was a man of great pride, that his calm, firm gaze seemed to reflect thinking on an elevated plane, and that the harmony of his facial expressions and bodily movements resulted in an overall effect of unquestionable candoraccording to the findings of physiognomists, those analysts of facial character.
Austin, the protagonist of Hollow Places, has an enormous distaste for this train of thought, thinking it to be one of peoples' main faults. It's clear this pet peeve stems from being judged by his own appearance. Austin himself is probably the most moral character within the novel despite having a body covered in burn scars and missing an arm.
Inverted in The Twits. Goodness equals beauty. Mrs. Twit was once a beautiful woman, until she started thinking ugly thoughts which led to the transformation into her hideous appearance. The narration states that people who are ugly can still have beauty shine through if they have pleasant thoughts and demeanor, accompanied by a drawing of such a person.
"You can have a wonky nose and a crooked mouth and a double chin and stick-out teeth, but if you have good thoughts they will shine out of your face like sunbeams and you will always look lovely."
Subverted in the school chapter of Buddenbrooks. In Hanno's class there's the student Wasservogel who's described as very ugly, but all the teachers treat him very generously to prove to themselves and the world that they don't fall victim to this trope.
Count and Countess seems especially fond of averting and subverting this. Vlad Tepes and Sultan Mehmed are given physical descriptions that sound very attractive, but the former is an utterly repulsive human being while the latter flip-flops between Magnificent Bastard and Chaotic Neutral. Elizabeth Bathory, the most sympathetic character in the book (though that's not saying much), sounds plain by her own description, or even ugly. Vlad is in love with her, though, so he only sees her as beautiful.
In Divine Blood you have HelLogesdottir, who is a cripple with her left arm and leg being withered and non-functional and the left side of her face likewise being paralyzed and withered. On the one hand, she's a bit caustic, and downright rude, referring to one of the other characters as "deep one" soon after meeting her. She's also a Demoness with a bit of an ego. However, she is decidedly not evil and ends up being the Damsel in Distress for part of the plot.
At the same time you also have Lady Tinia who is angelic appears through most of the story as a beautiful, stern blond woman wearing a pristine white trenchcoat. She's the bigoted Captain of the Tinia Royal Guard and is thus one of the two competing antagonists of the first novel.
Averted in Dragon Bones: The nobles Tisala of Callis, as well as her father, Haverness of Callis, are described as having large noses and overall rather unattractive features, and they're both heroic. There is also the Beautiful Slave Girl Bastilla, who betrays the heroes. Some of the heroes are quite attractive, but this is described as something that affects their popularity with the opposite (or their own) sex, not as something that has any connection with their morality.
Subverted with Geoffrey ae'Magi in Masques. He is beautiful, and everyone loves him. Turns out he's very, very evil, and the love all the people have for him is caused by magic, too. Oh, and his looks, while somewhat natural, are improved by magic that stops aging. Played somewhat straight with the close-to-nature shapechangers, who are all potentially beautiful, as they can change their appearance at will, but not all do so. Aralorn, the heroine, is rather plain in her true form, and usually walks around like that, when she's not on a mission as spy. And then there's Cain, whose face is full of burn scars, but who looks like his father Geoffrey if he removes the scars with magic. For most of the plot he prefers to let the scars be and wear a mask. He's rather challenged in the empathy-department, but one of the good guys.
In Enchanted Forest Chronicles, almost all of the princesses, princes, and knights are described as being very attractive, but most are oblivious, self-centered, and generally useless. Some are shown somewhat sympathetically (at one point, Cimorene points out that it wasn't their fault they were raised to be so idiotic), but Cimorene's thick-headed unwanted fiance, Prince Therandril, is still one of the obstacles she has to deal with in the first book (he just can't accept that she won't marry him). In Talking With Dragons, the princess and knight that Daystar and Shiara meet are shown to be ridiculously incompetent to the point of it being hilarious, though they still have the redeeming feature of truly loving each other. Meanwhile, the books have a variety of magical creatures of various degrees of beauty, none of whom are universally good or bad (the last book states that even some of the wizards were on the side of the Enchanted Forest). In particular, the dragons are shown as being terrifying, but they're all intelligent and mostly pretty helpful, if one gets their respect.
Played with in Which Witch?, where Belladona, the only white witch, is also the only one who's beautiful and all the dark witches are incredibly ugly. However Belladona desperately aspires to be dark and Arriman, the greatest dark wizard of England, is noted as being very handsome. Not to mention the three-headed Wizard-Finder is very polite and kind (at the story's end, the heads discuss in detail how to look after Terrance) and the baby Kraken, while described as a tiny squid-monster, acts like a regular baby.
Zig-zagged in the Lunar Chronicles. Our heroine Cinder is considered disfigured due to being a cyborg but her appearance is otherwise average. Her stepmother and stepsister are described as beautiful but cruel and abusive, while the kinder stepsister is also pretty. Queen Levana is beautiful but it's only a Lunar glamor she's projecting and is possibly average-looking or even ugly. Played straight with the handsome Prince Kai, Cress and Thorne.
One Ghosts of Fear Street book has the protagonist acquire a Clingy MacGuffin whose owners turn out to be tentacled, sluglike aliens. Another alien who looks more humanoid shows up and ostensibly tries to help the protagonist. The fact that the slugs turn out to be the good guys, while the humanoid alien is an intergalactic criminal they're trying to catch, is meant to be a twist.
Often inverted in Agatha Christie novels, which are replete with examples of beautiful people using their looks to get away with a whole host of seedy behavior. In particular, in one of the few consistent tells throughout her writing, if the narrative goes out of its way to describe a young man as handsome or pretty, nine times out of ten, he's the murderer.
Used for tragedy in Frankenstein: The monster is a hideous ghoul stitched together from various corpses, yet is the most warm, kind-hearted character in the book... at first. The people he meets are unable to see past his exterior and, with the obvious exception of the blind man, assume his heart is as ugly as his face. Over time, this mistreatment twists him into the very thing people assume he is.
Matelda is just a beautiful woman wandering through the woods, but she earns the trust of some strangers because they think her looks evidence her pure heart. As a servant of God, Matelda proves them right.
As Beatrice ascends closer to God throughout Paradiso, she becomes increasingly beautiful until her smile would crack a human's brain and her face defies all description.