The Pesger in Ancillary Justice. They have an odd view that any species they deem "significant" is inviolate and force all significant species to sign treaties to enforce their view, and they have the technology and military might to ensure those treaties aren't violated without serious consequence. The treaties leave justifiable reasons to kill members of a significant species, but they are so complex and unintuitive to a human mind that most people are unwilling to deal with aliens for fear of violating some seemingly-minor rule.
The Liaden abide by a strict, voluminous honor code that governs all aspects of their life and can seem cryptic and impenetrable to outsiders. Prominent features of this code include the concepts of Balance, which holds that any action (whether harmful or beneficial) must be met with an equivalent response, and melant'i, which crosses "face"-like social status with separation of multiple roles held by a single person. This code also incorporates different dialects of the Liaden tongue (which are spoken in different social situations) and bows of varying depth and associated gestures that convey relationships. On Liad, a social faux pas can have lethal consequences.
The Yxtrangi also have a very codified caste and honor systemóto Nelirikk's sorrow.
In fact, most planets and cultures in the Liaden Universe have their own cultural mores and honor codes that visiting characters find strange (and vice versa). One of the themes of the series is the difficulty outsiders can have in dealing with "local custom."
The Sidhe of The Dresden Files seem to fall into this category, though one went mad because she began to comprehend human pain (and this in turn led her alien mind to try and create a global catastrophe to stop the pain). Lea especially falls into this, as she wants to turn Harry into a hound because she genuinely thinks it would be the best way to protect him. She made a promise, in fact.
While on the Neil Gaiman track, God in "Murder Mysteries."
Raguel:(to God) Everything happens for a reason, and all of the reasons are yours.
For that matter, something similar came up in Good Omens, from Crowley: "It can't be a cosmic chess game, it has to be just a very complicated game of Solitaire. If we could understand we wouldn't be us."
The Aelfinn and Eelfin ("snakes" and "foxes") in The Wheel of Time series, another variation of The Fair Folk, are described like this: not even really evil, but so alien that they might as well be.
The citizens of The Capitol in The Hunger Games are appalled by bad manners but perfectly okay with 23 children being slaughtered in an annual fight-to-the-death for The Capitol's entertainment.
In Rikki Simon's Ranklechick and his Three Legged Cat the ghouls living aboard a space-bound zoo make decisions based on social awkwardness and individual instinct. Some are obsessively curious, some invent things for no reason, some live for the sole purpose of stopping the living space-station from killing itself. DaiLuvMoo, one of the ghoul-generals, seems to judge things based solely on how unreal he feels life is that day.
Merlin in That Hideous Strength provides Deliberate Values Dissonance to the post-Roman Christians with his at-times alien morality system. In one scene, Merlin believes Jane should be executed because she has unknowingly prevented the birth of a saint— by using birth control. Not abortion, you understand: birth control. He says outright that she is worse than Balinus, the hot-tempered Knight of the Round Table, who accidentally killed his brother in heat of battle and so started a feud that played into the downfall of Camelot. In his essay "Religion and Rocketry," Lewis touched on this trope by discussing the theological problems that would crop up if we found aliens. Their system of morality might be so incomprehensible to us that we would mistake them for evil.
In one of S. P. Somtow's Mallworld stories, an alien race hosts a banquet for their human hosts, featuring one of the race's prized delicacies. The primary ingredient for this delicacy was roasted alien baby (the children of this alien race were considered vermin until they reached a certain age). The aliens couldn't quite understand why the humans were so horrified.
In one of Larry Niven's Draco Tavern stories, a crewman from the first embassy ship to an alien homeworld reveals that when the aliens took DNA samples it wasn't for pure scientific purposes: they grow brainless human clones as a food delicacy. The UN quietly accepts royalties, and some of the crew members later kill themselves.
The Bishops in Future Boston don't consider their offspring to be fully "people" until they pass a sapience test. For them to eat one of their own children before that point would be considered merely bad manners.
In Larry Niven's Known Space stories, the moral code of the Puppeteer species is based on cowardice, manipulation, and paranoia to such an extent that blackmail isn't considered immoral — but bravery is considered insanity. In addition, they are capable of manipulating whole other species to promote their own interests, and don't think twice about doing it because they wouldn't think twice about doing it to another Puppeteer. They are called Puppeteers for a reason, after all.
The short science fiction story The Dance of The Changer and The Three is about a legend from an alien race of Energy Beings; the narrator, a human, cannot fully understand their motivations very well, in particular why they attacked the humans they had befriended; when asked why, their answer was "because." Moreover, the whole point of the legend/history referenced in the title, and why its protagonists are remembered and revered, is that they failed. Which by the point you find out seems almost comprehensible to the reader.
Perdido Street Station: The Weavers don't have a sense of morality as we would understand it, but rather a sense of beauty. That which is aesthetically pleasing or poetically appropriate to the Worldweave is "good" whereas that which is ugly or discordant is "bad." They can also disagree with one another and their aesthetic sense is incomprehensible to people. The humanlike races are deeply uncomfortable dealing with them because Weavers are so utterly unpredictable; they might help you, but they're just as likely to messily shred you and arrange your guts in a pattern that pleases them.
The Atevi in the Foreigner series have this. They can't understand the concept of friendship, but have their own biologically-based, heirarchical system of loyalty called man'chi. This tends to creep out most of the humans which landed on their planet (to be fair, humans generally make Atevi uneasy as well), so they designate a single human ambassador for when they have to deal with each other and keep well apart otherwise. This is, naturally, our protagonist.
Cherryh also applies this trope heavily in the Chanur series; the methane-breathers are considered unpredictable by Hani for good reason. Especially the Knnn. Not that the other oxygen-breathing species don't give a decent Hani captain trying to figure out what makes them tick their own share of headaches, mind, but at least those can be talked to in a more or less straightforward fashion. The most accessible methane-breathers, the Tc'a, have five brains in one body and a language that's best translated into a word matrix that can be read in multiple directions on a convenient screen.
While the Otherness in the Repairman Jack novels is a fairly standard Eldritch Abomination or group thereof, what exactly motivates the Ally to oppose it is very uncertain.
The Third Men in Last and First Men are essentially a species of esthetes. At one point their world was dominated by an empire based on music. Their final civilization was obsessed with biological manipulation: one faction used to breed ever more powerful diseases and parasites on the grounds that when a "higher" lifeform is slain by a virus, it has a certain ironic beauty.
Robert A. Heinlein was particularly well known for his ... interesting takes on morality throughout his works.
The Martians in Stranger in a Strange Land have an understandable morality, but it's essentially incompatible with how we view it. One of the biggies that is only mentioned in passing is the idea that putting someone in prison is a horrible, horrible thing to do. You should just kill them instead. Also, they're very strongly for cannibalism as a nearly religious rite.
That could be why the main character in the story who was raised on Mars breaks into a prison, uses his abilities to end the existence of the worst offenders, and then erases the bars in a similar fashion, thus setting everyone else free. He just eliminates anything that he thinks should not exist, including certain people.
A few other tidbits: they can't fathom hate or dislike anyone or thing with more than a "mild distaste," this is because they devote so much time to understanding things that they can never truly hate it. Also, they see no wrong in obliterating planetary civilizations if, after centuries of contemplation, they decide it necessary, as they did with the fifth planet in our solar system. No, not Jupiter, the planet that is now the asteroid belt.
Martians in Double Star have a highly complex system of politeness note From their physical description, it could be inferred that these are the same Martians from Stranger in a Strange Land above. The main problem of the book is that a politician may be late to a ceremony that inducts him into a Martian clan. There is a legend on Mars about a young Martian who was late to something important, and the consequence of this is death. He was given a second chance, on account of being young and having only a partially formed brain. He would have none of it, so he brought a case against himself in court, successfully prosecuted himself for being late, was consequently executed, and is now held in reverence as the patron saint of propriety on Mars.
In Space Cadet, eating in public is the big taboo on Venus.
In Glory Road Star is shocked to find out that sex is a sellable commodity in Oscar's reality. In her world, a woman's sexuality is considered an integral part of her spiritual existence and it cannot be bought and sold, only partaken of as a gift of the woman.
She's also horrified to find out that Oscar turned down the sexual advances of their host's daughter and wife the night before. While he thought he was protecting the sanctity of his host's home and family by not taking advantage of the man's family, their host was so insulted that he turned down their gift that he expelled them from his home at first light.
In Magic, Inc., the salamander who helped in the destruction of Archie's business cannot be yelled at or punished as the other fantastical beings can. It has no sense that what it did was wrong, just that the person who asked it to do so provided something entertaining that it was inclined to do. Archie offers it a special fire place in his home to gain its favor and encourage it to do what he wants.
Catch-22: Milo Minderbinder. It's not just that he believes anything that promulgates capitalism to be good. It's that he has absolutely no comprehension of how anything that promulgates capitalism could possibly be bad.
This is the way the Elder Gods and Old Ones of H.P. Lovecraft's Cthulhu Mythos work. They seem malicious, but they're simply so far beyond human comprehension that our concepts of good and evil cannot be applied to them. Works based on Lovecraft's universe tend to make an exception for Nyarlathotep, as someone who can operate on a human level and shows clear sadistic tendencies.
"The time would be easy to know, for then mankind would have become as the Great Old Ones; free and wild and beyond good and evil, with laws and morals thrown aside and all men shouting and killing and revelling in joy. Then the liberated Old Ones would teach them new ways to shout and kill and revel and enjoy themselves, and all the earth would flame with a holocaust of ecstasy and freedom."
The Mi-Go from The Whisperer In Darkness consider it a reward to extract your brain, put it in a jar, and take you on a cosmic sightseeing tour.
The Elder Things, on the other hand, are a massive subversion. They are by far one of the most bizarre species to come out of Lovecraft's mind, but their interests, desires, and needs are readable enough that a human can piece together their history from the bas-reliefs they used to decorate their houses. One of the people studying their ruins calls them "men of a different kind", despite their vastly different physiology and being long-vanished before the first ape hit another with a sharp rock.
The sphinxes who guard the first gate in The Neverending Story. Most people who attempt to pass them are instantly paralyzed and no one has been able to discern any pattern concerning who gets to pass.
In the film, the gnome states that the sphinxes strike those who do not feel their own worth. Although it later turns out that it's more "those who fail to dodge".
The Childlike Empress herself also qualifies. She is described as being something above and beyond any creature of Fantastica; for her, all of her creatures good or evil are equal, and she doesn't hesitate to send Atreyu to a life threatening adventure if it suits her purposes. Neither she will later come to the help of Bastian, even when he is in danger of losing all his memories and ending up as a resident of The City of the Old Emperors. For us, outside readers, her acts may sometimes seem like she doesn't care for anything, evil or just outright inexplicable.
The Elohim from the Chronicles of Thomas Covenant straddle this and Above Good and Evil; since they are Earthpower incarnate and able to see and understand nearly everything they frequently act in ways that are incomprehensible to us mere mortals. To top it off, they also tend to say that anyone who isn't an Elohim can't even think about judging them and their actions. Bastards.
From the same series, the ur-viles. Initially introduced as Always Chaotic Evil, it's revealed they they're an artificial race created by Black Magic, and consider their own existences to be abominable. Everything they do is based around attempting to create some purpose for their lives- whether that purpose be good or evil. As of the Last Chronicles, they seem to have chosen good.
Tom Bombadil from The Lord of the Rings is considered to be something of a mystery by the people of Middle Earth. No one really knows who or what he really is, while Treebeard (who was around before the First Age) has stated that Tom was on Middle Earth long before anyone else. He ultimately comes across as something of a True Neutral who exists outside of the conflict between good and evil: though this makes him the only character in the original story who could outright ''ignore'' the power of the One Ring, it also meant that he was incapable of possessing it as well. At the Council of Elrond in Rivendell, the possibility of giving the One Ring to Tom Bombadil for safekeeping is rejected by Gandalf, on grounds that he was incapable of understanding this responsibility, and would end up either losing or even discarding the Ring out of carelessness.
The Inchoroi from R. Scott Bakker's Second Apocalypse series (more commonly known for the Prince of Nothing Trilogy) qualify for this trope. They are described as being a "Race of Lovers," by which they mean a race "given wholly to their lusts," for whom the vagaries of ejaculation and their lust are king. It was presumably a nasty shock for them when they found themselves stranded on a planet where Old Testament Morality — including damnation — is objectively real, meaning that the species is doomed to burn in hellfire for eternity upon death.
The Dunyain monks also have a very alien concept of morality. The goal of their organisation is to create a "self-moving soul," a being with absolute free will. In the meantime they consider everyone else to not be autonomous beings but rather slaves to circumstance. Therefore the Dunyain have no compunctions about manipulating people however they like and genuinely see nothing wrong with it.
Sergey Lukyanenko's Genome trilogy features Brownies, aliens whose behavior is completely insane by human standards.
Lukyanenko absolutely loves this trope and uses it whenever possible. For example, in one of his first major works, The Lord from the Planet Earth trilogy, there were Fangs — a race of aliens who judged anything by its ''aesthetics''. So, upon learning the War Is Glorious trope from humans, they though that humans would be good sports and immediately went to war. When they found (from the main character, incidentally) that humans also think that the War Is Hell, they were utterly dumbfounded by such seemingly schizophrenic (to them) thinking. And that's just the least bizarre example.
Their morality was a mystery to most humans for the longest time. It was only the protagonist who finally figured it out. It's likely that the first human ships that discovered the Fangs had videos and pictures aboard that resulted in the Fangs assuming that war and torture are beautiful by human standards (after all, why would anyone put something into an art form if they didn't think it was beautiful). They proceed to mutilate and kill most of the crew. At the end, the protagonist is engaged in a duel to the death with a Fang soldier, who's much better at him. Just as the Fang is about to strike him down, the protagonist notices that he left himself open to a cowardly attack. Why? Because no Fang would take advantage of this. Being a Combat Pragmatist, the protagonist deals a mortal blow to the Fang using this method with all the other Fangs monitoring the combat. Thus, this cowardly (i.e. ugly) strike finally teaches them that they were wrong.
The various magical creatures of the Harry Potter universe tend towards this. The house-elves are the most obvious, being extremely powerful magical creatures who just want to care for humans,which leads to the elves being abused, but most of the others also have values humans don't understand. Centaurs are skilled in predicting the future but disinclined to interfere with it. Goblins' law holds that an item belongs to the goblin who made it - anything purchased from a goblin is in their view a lifelong rental, and should be returned after the buyer's death; this view plays a role in the plot of Deathly Hallows with Godric Gryffindor's Goblin-made sword.
The Ellimist from Animorphs comes off like this in his first few appearances, with apparently self-imposed "rules" governing how he can interact with other species that he nevertheless finds ways to bend. The pattern becomes more logical when we're introduced to his Evil Counterpart, Crayak; the Ellimist needs to follow his "rules" to avert an all-out war with Crayak (which would likely destroy the universe), but he's clever enough to still work things in the Animorphs' favor.
Crayak's own Howlers turn out to function on this. They are intially perceived by the protagonists as savage xenocidal hunters who are Crayak's personal killing tools, but when Jake morphs in a Howler, he's surprised to find that it has the mind of a playful child, and killing is just a happy game to it.
The microscopic Helmacrons also come across as this. Their two ships try desperately to kill each other off, but once one ship is destroyed by the Yeerks, the other Helmacrons immediately attempt to avenge their deaths. They kill all of their leaders, because any leader who makes a mistake would have to be executed, and "This way she may be a symbol for all to admire." And the females severely oppress the males, so Cassie and Marco decide to give the males a pep talk about gender equality. When the Helmacrons next appear, it seems the Animorphs may have inadvertently started a civil war, with the males and females each trying to wipe the other out.
The Skrit Na seem to be this not only in comparison to humans, but in comparison to every major sentient species with space travel. Nobody even tries to explain their actions to the reader beyond describing a few random behaviours (like picking up aliens, flying around with them for unknown reasons, and then dropping them off again), and claiming that the Skrit Na are impossible to understand and their behaviour doesn't seem to follow logic.
The Iskoort have an extremely unusual moral system, as well as an unusual planet in general. Their caste system would be unworkable in human society, but works fine for them, because their rules are so different. To an Iskoort, 'good' is a question of fulfilling your caste role — not necessarily to the benefit of society, just to the extreme of the behaviour proscribed by the role. Warmaker Iskoort look gruff and beat people up. Salesmen Iskoort aggressively sell anything and everything to anyone and everyone, including attempting to buy the organs of living aliens and split the proceeds with their heirs. Shopper Iskoort shop. Their function is to just buy things all their lives, to no obvious purpose other than creating capital flow and a marketing focus for the salesmen.
In Star Trek: The Lost Era, we're introduced to the Manraloth, whose hat is skilled communication and manipulation, and who use these skills to aid in bringing peace to the galaxy. Their methods of doing so conflict with those of the Federation, and they are very, very sneaky and manipulative. Always, though, their intentions are good and noble. The same novel which introduced them also introduced another Blue and Orange Morality culture to the Star Trek Novel Verse: The Regnancy of the Carnelian Throne, whose citizens are metaphorically slaves to the Carnelian Throne itself. They ritualistically "play along" with subjugation as part of their "enslavement" to the values it represents. In another Star Trek: The Lost Era novel, The Sundered, Sulu acknowledges this trope when agreeing to honor the Tholian warrior caste's legal determinations of truth, which are arrived at through combat.
Funnily enough, that last bit about the Tholians was also sometimes used during the middle ages. For a time it was perfectly legal for the two parties in a case to have a fight to the death. The idea behind this was not that strength implied truth, but that God was just and thus would not let an unjust person kill the just person.
Introduced in Star Trek: Ex Machina are the Shesshran, who operate somewhat differently from Humans, and most other races. They are unashamedly belligerent without apparent motive, and like shooting at things to say hello. They fantasize about killing their own children and generally behave in a bloodthirsty fashion. They're actually quite reasonable and honorable beings — it's just that they are naturally highly individualistic predators, with strong hunting instincts. They reject all hierarchies and authority, and view the universe through the eyes of a lone predator.
And while we're in the Star Trek Novel Verse, the Pahkwa-thanh have always considered their prey animals sapient. They don't eat humanoids and "civilized" beings, not because they have an objection to it as such, but because it would be rude. Humanoids don't consider themselves part of nature; to eat them would be impolite, which Pahkwa-thanh are not. If you think you're prey, though, they'll happily eat you. The Frills are another more-or-less-friendly race that is happy to eat sapient prey. Both Frills and Pahkwa-thanh are Federation members.
In Footfall, by Larry Niven and Jerry Pournelle, the aliens and humans really don't quite understand each other's psychology, mainly because the aliens have much more of a herd dynamic. Most relevantly, the aliens don't understand how or why you would possibly initiate diplomacy before first fighting to see which party was dominant. Likewise, they don't understand why a battered humanity responds with total war (an unknown notion to them), rather than taking a Defeat Means Friendship-type submissive relationship.
Quantum Gravity: The premise is that humans are dealing with The Fair Folk ("Yes, I'm probably going to try to trick you. You weren't expecting that?"), Demons ("Everything is an art.") and Elves ("Allegiances are not simple." + incredible patience), and some beings which may or may not have a traditional consciousness. This is par for the course.
One fairy comments that she prefers working in adult films with demons because their hearts are pure.
Dar tortured Lila for information he and those surrounding knew she did not have. This makes perfect sense to most elves.
In an example of etiquette, rather than morality: Elves live for a very long time, and so are patient. They will just wait for you to finish or do otherwise. Humans see this as infuriating, because it looks like the elves don't care about anything. Elves find the human way of conversation annoying to a little childish, though they usually understand.
The author has a segment where the readers are allowed in Zal's head, and see why he got together with Lila—he didn't want to fall in love with anyone he could lose, but Lila was lacking enough in self-confidence to not want to leave him, and tough enough that it'd be hard to take her from him. The author presents this sympathetically ... and it works.
In Speaker for the Dead, several pequeninos are ritually murdered by their peers for providing important conceptual or technological advances. This only gets figured out when humans realize that, due to the piggies' Bizarre Alien Biology, My Death Is Just the Beginning. After a piggy is ritually executed, they turn into a tree. The males can only have children after becoming one, in fact. Unfortunately, disaster strikes when this ritual vivisecting gets done on humans...
The Bugger Queen is another prime example, lacking a real concept of murder or death because of her sole interactions with hiveminded soldiers who are (or have at least been bred and controlled to be) as expendable as a toenail or a strand of hair. She eventually learns to interact with other species without doing anything too monstrous, but in accordance with her alien morality refuses to really intervene for anything but the prevention of genocide and shows no real deference to the safety of individual humans.
She also doesn't really care whether or not she herself lives or dies, as long as at least one of her daughters (another Queen) survives somewhere.
In The Sparrow, breeding rights are a huge deal because it would be immoral to just let people breed wantonly and possibly over consume resources. This strict focus on population control and the human misunderstanding as to the levels the Jana'ata will go to maintain it ultimately causes the catastrophe at the end of the book.
In In The Cube, multiple alien species with this mindset interact with humans, often with confusing results. The beaver-like Phner, for example, don't consider anything to be aesthetically fulfilled until it is destroyed, hence quickly demolish any artwork that comes into their possession. They dissect their dead in a funerary celebration, to better appreciate every last iota of the dead Phner's identity and experiences.
In Future Boston, which is set in the same universe, there's an alien called The Bishop who puts everything in three categories: sapient, food, and inedible by reasons of insanity (anything not yet proven sapient). He casually mentions how he will eat his children if they fail a test.
The Wess'har in Karen Traviss' Wess'har War series who have no concept of a "grey area," have no interest in the concept of motivation and have two different concepts of sex, sex and ouran, both of which to human eyes look like...sex. Also no concept of embarrassment. They are also natural "small c" communists with no need for a compelling authority.
In Gordon R. Dickson's The Alien Way, there's a race with a strange "honor" code, which considers perfectly honorable to kill your mates, friends and family members, if it helps you to gain power or opportunities to spread your genes, and the closer you are to the person killed, the more honorable the act.
As long as you are completely successful in achieving your goal; if you are not completely successful, you are killed. In the story, the protagonist is revealed to have been captured and released after his recording device had a prepared sequence played into it; because he only returned because he was allowed to believe he had successfully escaped, he was killed as a failure by the tribunal reviewing his actions. And he went to the tribunal knowing that he would almost certainly be killed for revealing the addition to his recording, but recognizing that it was essential that they be made aware of the information.
Some of the acts depicted in the Reynard The Fox fables are pretty horrific by today's standards. For example, Reynard is about to be put to death for committing numerous crimes against the other animals. But Reynard convinces the royals to let him go by playing to their greed and promising treasure. Reynard requests that two of his rivals, Isengrim and Bruin be partially skinned alive so that the fox could wear their pelts for the trip. King Noble, who is supposed to be a figure of benevolence actually grants Reynard's request.
Reynard the Fox also contains a heaping amount of Carnivore Confusion. Though the animals are supposed to be sentient, they are depicted as being still wild and retaining their animal instincts. This makes Reynard, who kills and eats several young chicks, the animal equivalent of a baby eating anti-Christ among the other animals.
It is actually more accurate to say that the angels have never eaten from the tree of knowledge, as Adam and Eve did. Therefore they can commit sins the way humans do, but have no knowledge of what sin means and thus it is meaningless to them. It may make human morality a fair example of Blessed with Suck.
Warbreaker's Nightblood is a sentient weapon created with the express command to destroy evil. The problem is, a sword has no brain with which it can understand what evil actually is, let alone some mystical way to Detect Evil, so it just kinda guesses. The result tends to leave a lot more people dead than it ought to.
Nightblood: I'm not evil. I destroy evil. I think we maybe we should destroy those men up ahead. They look evil.
In Clive Barker's The Hellbound Heart (which eventually became the basis for Hellraiser) the Cenobites are examples of this trope: they have explored pain and pleasure to such an extent that their understanding of either is almost incompatible with that of most human beings, which leads to trouble when people try to contact them in order to take advantage of the "pleasures" they can offer. All in all, the Cenobites do not appear to understand or care that their charges are in agony most of the time- after all, they did ask for it, and if they aren't enjoying themselves, they'll just have to learn how to do so.
Frank even reflects at one point that on how stupid it was of him to summon them without first finding out if their definition of pleasure coincided with his own.
Human morality is very strange to treecats in the Honor Harrington series. For one thing, the 'cats consider a desire for physical privacy to be just plain weird. They're telepaths, so it makes sense. Also, they have a code for dealing with anyone who actually manages to make an enemy of them that does as follows: There are two types of enemies; those that have been properly dealt with, and those that are still alive. Fortunately, they're a laid-back species.
The Spider-wolves look ugly as sin but their ships and formations are a thing of beauty, and they don't mind helping humans.
A relatively mild example is P. G. Wodehouse's Jeeves; he has no problem with his employer Bertie Wooster drinking heavily or committing blackmail and burglary, but no mustaches or frilled shirts will be tolerated.
For the LodgelessOnes in Marti Steussy's Forest of the Night, building a permanent shelter is a no-no. Calling someone's autobiography "boring," or accusing them of embellishing it, is fighting words. Letting your disabled child starve to death because he can't hunt is unfortunate, but not morally wrong. Eating your child's corpse? At least the scavengers didn't get him.
In Harry Harrison's The Jupiter Plague (AKA Plague from Space), a strike team breaks into the quarantined spaceship and finds the recordings of the mission on Jupiter. They find out that the crew discovered an alien race living on the solid core of the planet. Unlike humans, the "Jovians" use biotechnology. They initially offer to talk to the humans but then proceed to slaughter most of the crew in increasingly gruesome ways. Their latest act is sending the human ship back to Earth with a genetically-engineered virus that easily jumps species and is 100% fatal. It doesn't take long for the protagonist to figure out why they behave this way. Apparently, the Jovians are a Hive Mind species, where each being is but a cell in a larger organism. As such, they consider humans to be the same way, and all their murders are merely studies. After all, what's killing a few cells to a giant organism? It is not revealed if the Jovians finally realize the error of their ways or not. They do provide humanity with a cure after they complete their study, though.
On the one hand, the human strike team threatens the Jovian they find in the shipnote by saying they'll cut the communications link to Jupiter - the individual Jovian isn't important to the Hive Mind, but the experiment is into giving up the cure. On the other hand, the cure turns out to do more than just cure the Jupiter Plague.
Comes up in works by M.C.A. Hogarth, who describes herself as "an anthropologist to aliens". Examples include the caste system and community-orientedness in Kherishdar, or the fact that the Jokka completely separate procreation and love (which is taboo if it is between different genders).
Chiun from The Destroyer is from a village that has fed itself through the ages by hiring out as assassins, because of this assassins are greatly respected in the village. The only target that is forbidden is children. They revere many of the great tyrants of history because they provided a lot of work and thus helped support the village. Lee Harvey Oswald's killing of President Kennedy is shameful only because he was an amateur: he was not paid for it and he used a gun instead of bare hands.
As with many other depictions of The Fair Folk, fairies and similar beings in Fablehaven have very alien concepts of morality. Several of them, for example, don't see anything wrong with killing humans just because they can, because human life is so short anyway. (In-universe, it's likened to a human stepping on a bug.) And that's only the least of it. With few exceptions, however, the humans don't treat this as bad—it just means they need to be exceptionally careful around them. One of those exceptions being centaurs, whose obfuscating jerkassery is treated as exactly that.
It's even discussed in the third book, when a plague is changing creatures of light into creatures of shadow. Grandpa points out that the light creatures are easily corrupted while the humans are largely unaffected because they are not good by nature, they just act on instinct. Warren points out that, while the philosophical implications are all nice to discuss and all, they have a powerful enemy at the moment.
Warren: If a starving bear ate my family, I would understand why it did it. That doesn't change the fact that I would still shoot it.
Subverted with the Marat, Canim, and Icemen in Codex Alera, who are initially considered too alien to coexist with humanity in-universe, only for a good chunk of the series to involve The Hero finding common ground and building bridges with them. Played completely straight with the Vord.
In the short story "The Moon Moth", musical virtuosity and swordsmanship are the basic virtues, money is meaningless, and everyone must wear a mask at all times. Protagonist Edwer Thissell uses this against antagonist Haxo Angmark in a beautifully absurd, yet appropriate, conclusion; when Angmark desperately accuses Thissell of having kidnapped, murdered, sold children into slavery, an angry onlooker replies: "Your religious differences are of no importance. We can vouch however for your present crimes!", and the crowd kills Angmark for alleged violations of local morality: trying to remove someone's mask, insolent behavior, and the like.
Or as frequent Vance protagonist Magnus Ridolph wrote: "In all the many-colored worlds of the universe no single ethical code shows a universal force. The good citizen on Almanatz would be executed on Judith IV. Commonplace conduct of Medellin excites the wildest revulsion on Earth and on Moritaba a deft thief commands the highest respect. I am convinced that virtue is but a reflection of good intent."
In The Otherworld, werewolf Clay was changed at age five instead of late puberty like almost everyone else, and then left on his own for two years. As a result, his thought processes are much more wolflike. His morality centers around what's best for his pack, with an afterthought of what will make his mate happy. Clay brutally tortured and murdered one werewolf threatening his pack and distributed the photographs freely to discourage others from trying, but the thought of killing people needlessly or for fun revolts him. He wouldn't stop to help an injured stranger - unless his mate was watching - but he has laid down his life multiple times without hesitation for his packmates.
In None But Man this is the very heart of conflict between the humans and Moldaug. While humanity judges every action based on whether it is Right or Wrong, the Moldaug judge their decisions based on whether it is Respectable or Not Respectable. Earth's government is willing to capitulate completely to avoid a war, but the sheer lack of Respectability and hints of even worse acts to come from such an action would compel the Moldaug to destroy humanity.
In Dirge for Prester John John's moral standards are perverse and inexplicable to the people of Pentexore, as are their moral standards to him.
Andrew Vachss's Burke books often go into how the minds of criminals are not just looser in morals but outright Different from that of citizens.
Lady Lilith of Witches Abroad thinks that bringing about fairy tale plots is a good act regardless of what the other people involved want.
The city in the Redfern Barrett sci-fi short story Transaction has a strange set of moral principles, unsurprising considering every possible interaction involves a transfer of money.
In the short story The Chinago written by Jack London and set in the early 20th century, the Chinese protagonist Ah Cho can't understand why the French Colonial authorities refrain from simply using torture to solve a murder.
From the Hannibal Lecter series, Hannibal Lecter, Jame Gumb and Francis Dolarhyde. In the first two books, the POVs for all three serial killers (Dolaryhde, Gumb and Lecter) demonstrate that they have completely alien personalities and outlooks on life. They are not simple Card Carrying Villains so much as they are living in a terrifying fantasy world of their own creation where nobody else is a real person and their every thought reflects their twisted pathologies. At first, this might seem over the top, but the longer you stay with them the more it becomes flat-out disturbing and outright freaky.
In Evolution there are several instances of infanticide (like when a tribe of hunter-gatherers take a newborn baby and bury it alive as a form of population control), genocide of other tribes, and rape. All explained in detail with the cold logic of survival and passing the genes to the next generation.
Kroniki Drugiego Kręgu has numerous differences between human and dragon cultures:
Human telepaths see entering minds without permission as a violation. Dragons, which use telepathy on a daily basis, donít have such limitations, generally Cannot Tell a Lie and speak their mind even if what they think is rude or offensive. One human character who adapts these rules is seen as rude and antisocial by her fellow humans.
Dragons see gold as pretty but useless and already owned cow as a prey waiting to be killed not someone else's property.
Humans tend to burn or bury their dead and see dragon custom of eating their loved ones as barbaric. Dragons see human burial ceremonies as wasteful. One dragon character cannot wrap his mind around this, until he finally decides human use fire to make their dead more tasty.
Dragon has different concept of time because of their longlivity.
Brave New World could be considered an example. The word "mother" is obscene, sex is as impersonal and quick as a handshake, and Romeo and Juliet would be considered a comedy.
The Philip K. Dick short story "Rautvaara's Case" was about trying to blend the religious beliefs of a human with that of a race of plasma lifeforms. The results are pretty Squicky, as the aliens believe that immortality is gained through their savior consuming them (depicted as being the opposite of the Christian belief of Communion), which ends up with the eponymous character watching in horror as Jesus eats her crew members.
Science-Fiction 101: In The Monsters by Robert Sheckley, a disastrous first contact scenario is described that stems from a lack of understanding each species's morality. The native species practices gendercide, giving a wife twenty-five days to live before killing her, and treats debates as Serious Business, killing anyone who uses faulty logic or contradicts their partner. It turns out that this is their mechanism to curb overpopulation, as their species has eight females born for every male birth. The visiting astronauts find this practice horrifying, especially when the natives try to "help" by killing the alien females! And then disaster breaks loose.
The dolls of The Dollmaker make very little distinction between sex and murder.
The Twins in the League Of Magi are completely baffled by the idea of using their nigh-godlike power to save some people they've unknowingly endangered. They are weirdly motherly toward their wendigo, though.
For the Shongairi from Out of the Dark, refusing to submit to an obvious superior, especially after that superior has demonstrated unquestioned strength, is horrific. They also don't see why humans get pissed when Shongairi eat the corpses of those they killed, including children; to the Shongairi, eating the corpses is the only way to honor them and not let the soul go to waste. Humanity's refusal to back down and fight viciously out of a need to protect their families or to seek vengeance for the deaths of loved ones is utterly alien to the Shongairi.
Willy Wonka in Charlie and the Chocolate Factory (and its many adaptations) has this as part of his highly eccentric nature. He is a cheerful, pleasant person most of the time, but disobey his rules and he holds no sympathy for what might become of you — he's often amused by the results — though he will try to get you back to normal. To make matters worse, he has a...habit of metaphorically dangling dangerous things that you find yourself irresistably drawn to within reach, possibly deliberately testing your willpower and/or leading you into a trap. He's generally more concerned with his inventions/sweets than with people. His workforce consists of a transplanted tribe of doll-sized people whom he convinced to work for him — work that includes being test subjects for potentially dangerous inventions — by agreeing to let them have all the cacao beans they wanted (as they're highly craved by them) in return. His Mad Scientist sensibilities and sense of aesthetics trump conventional concerns for safety: In the novel's sequel the process of perfecting a fountain-of-youth pill involved testing it on over 100 Oompa-Loompas, and at that point the pill was too strong and de-aged them out of this physical plane (though he did eventually rescue all of them by creating an aging counterpart). And because he's Inexplicably Awesome and has no backstory in the novel, how he developed this morality is a mystery. General consensus is that he's a Jerk with a Heart of Gold if anything, but because his way of thinking is so off, he's an Interpretative Character highly subject to Alternative Character Interpretation from adaptation to adaptation.