The Eddorians from Lensmen. Eddorians originated from a parallel timeline where they reduced the entire universe to a lifeless husk by way of Planet Looting it into oblivion. In point of fact, the Eddorians don't consider themselves to be pirates (despite the fact everyone calls them that, and even their minions consider themselves pirates) because their civilization, top to bottom, is built on it. They view planets, galaxies and entire universes/timelines as nothing more than a finite resource to be devoured. They consider other races slaves at best and obstructions to their piracy at worst, and they actually cannot conceive of the notion of peaceful co-existence with other species. They basically either want to take everything you have, kill you, enslave you, or all three, and even their minions make the Reavers from Firefly look like they were Care Bears raised by Fluttershy. One of these minions thinks nothing of casually committing galactic genocide to fulfill the Eddorians' plans...and he's probably the closest to Affably Evil the Boskonian Pirate Cartel gets. Oh and did I mention, the Eddorians themselves are Eldritch Abominations that resemble immense, living tumors who reproduce via cell division and are so long-lived they literally outlived their universe?
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.
The Presger 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.
It's also implied that the Presger are psychologically incapable of understanding what humans consider natural divisions within a species (e.g. race and culture).
One of the Presger translators, humans made by the Presger to communicate with humanity for them, recalls being admonished not to eat her siblings. She did eat people, but no one she wasn't supposed to eat, so it's okay.
Discussed and ultimately subverted in Blindsight. Much of the early book is spent discussing the potential moral outlook of the Rorschach's creators, especially by Isaac (a biologist) and the Gang-Of-Five (who are sociologists and linguists) using their respective fields to argue for the degrees to which the aliens will, for example, obey human rationality like Game Theory or how belligerent they will be. Ultimately, it turns out the Scramblers don't have a concept of morality, or indeed a concept of anything — they're non-sentient and do everything unconsciously. Being self-aware is inconceivable to them, and thus they interpret humanity as trying to attack them by making them waste their time interpreting statements we've made from a sentient viewpoint.
In Chronicle of the Unhewn Throne There is the Csestriim, a race of essentially demigods. During one scene where two armies were facing off, it was thought to be an unwinnable battle, until the Csesstrim strategist showed up. Leading the "good" army for his own alien reasons, he gives confusing commands to various squads in his army, such as "Kill five enemies and then lay down your weapons and surrender." Sure enough, the battle was won.
In Brave New World the word "mother" is obscene, sex is as impersonal and quick as a handshake, and Romeo and Juliet would be considered a comedy. When John the Savage complains to Mond that the world feels so wrong, Mond argues that that's because John uses the old system of "right and wrong" as opposed to the new moral system of "happiness and unhappiness". The society in Brave New World is based entirely around the pursuit of personal happiness, extreme hedonism; to be dissatisfied is to be actually insane. This is presented as dystopia because while everyone is happy and youthful, their society stifles creativity, productivity and free will.
Andrew Vachss's Burke books often go into how the minds of criminals are not just looser in morals but outright Different from those of citizens.
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 who 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.
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.
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.
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.
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 Call of Cthulhu")
The Elder Things from At the Mountains of Madness, 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. He even realized that they're not the murderous monsters he first thought they were, since it's likely from their point of view they were killing in self-defense.
The Great Race of Yith from The Shadow Out of Time zig-zags this trope. They are a race of highly advanced aliens from some unknown star cluster that transplanted their minds across the void of space into the bodies of a bizarre species of alien that existed on Earth in its infancy, and also have the ability to send their minds across time, which they use to explore the era of Man, leaving the minds of the humans they transplant temporarily trapped in horrifyingly alien bodies. But the Yith also take care to make the time their prisoners spend among the Yith as pleasant as possible, and eventually erase their memory when they return to their own time so as not to cause further mental distress, and have built a very advanced, intellectually based civilization. Like the Elder Things, their desires and interests are relatable enough for a human being, even if their morality and intellects are vastly alien.
W.H. Pugmire, a modern Lovecraftian author, uses Perspective Flip quite a bit so that we see humanity through the eyes of some very inhuman beings. Basically, humans are ultimately insignificant in the face of cosmic magic but nevertheless fun to toy with (especially if you're Simon Gregory Williams).
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.
Gore Vidal's Creation shows the ancient clash of morality and ethics between the Persian, Greek, Indian and Chinese systems. With Buddhism in particular shown as being beyond human morality.
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.
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.
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.
The dolls of The Dollmaker make very little distinction between sex and murder.
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.
David Gemmell's Drenai books have the Sathuli, who have a terrible reputation due to torturing their captives to death; they believe this purifies the soul, and so their most respected adversaries receive the most agonising deaths. They also have religious objections to breaking bread with "unbelievers", but it's the torture thing that made them and the Drenai enemies.
Probably the single most important trope in Ender's Game and its many sequels. The Buggers/Formics have a morality not dissimilar to our own, but because of the way their society is structured (almost the entire population are mindless drones with only a handful of thinking/feeling "people" at any given time) and their inability to communicate with creatures as psychologically different as humans, it's virtually impossible for humans and Buggers to relate to each other in moral terms, or even grasp what the others' values might be. They eventually learn to cope, but it takes millennia and there's a lot of bloodshed in between.
The Formic Queen is another prime example, lacking a real concept of murder or death because of her sole interactions with hive-minded 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 one of her daughters (another Queen) survives, since her memories will be passed on via their hive-mind anyway.
In its follow-ups this tropes gets Turned Up to Eleven, as humans encounter even more baffling and incomprehensible creatures, including one species for whom ritual murder is an essential part of their reproductive process and another which is an intelligent (and terrifying) disease.
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...
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.
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 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.
The gods of Matthew Laurence's Freya series often have this trait due to their belief-driven natures. For instance, at one point Freya abuses her magic to essentially steal luxury items. She mentions feeling bad about it, but not because she's taking something that's not hers - she's offended she has to use her powers at all, as it implies she doesn't deserve those things for free to begin with.
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.
Holly Black frequently does this for her otherworldly subjects, most notably in her book The Darkest Part Of The Forest: The Fair Folk have no qualms about murdering tourists visiting the local town of Fairfold in gruesome ways, or else kidnapping human babies and replacing them with their own, i.e. changelings, for unknown reasons; other nasty habits of theirs throughout the book include cursing locals, or in the case of Ben, being "blessed" with a gift for fairy music that ends up backfiring on him when he grows older. To them, humans are basically ants and as such they feel they have the liberty to do whatever they like to them, which on a lucky day will mean all the milk in the house spoiling and in some of the worst cases being turned into a pile of rocks with the only way of breaking the curse being another human being recognizing that the "rocks" are actually a person (or people) under a spell.
Specifically invoked in The Dresden Files in the case of Bob the Skull. As a Spirit of Intellect, essentially a non-corporeal supernatural library with attitude, Dresden describes Bob as being extremely fuzzy on the entire concept of "good" and "bad." So when Bob describes an infamous necromancer as capital-E Evil, it makes Dresden sit up and take notice.
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.
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.
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 thought 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 than 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.
That Fang soldier was actually much smarter. He understood the problem perfectly and left himself open on purpose, hoping that the protagonist would use the opportunity and thus convince other Fangs.
Subverted in The Gods Are Bastards: There are a race of demigods who have trouble understanding human morality and appear to follow their own ethical system, based on "natural" principles. Over time, though, the characters figure out that they're basically just powerful humans who were never taught that other people had feelings.
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.
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 goes 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.
At least, they were laid-back until a Colony Drop wiped out an entire treecat clan. The rest of the species has strong views about what should happen to the humans responsible for that little incident.
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 Bishop 24 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. Just to keep things unpredictable, Bishop 24's criteria for whether something qualifies as "food" are partially dependent on how hungry he is at the moment.
In The Invisible Library, there are The Fair Folk, who seem to have no morality whatsoever, but if they have any it is probably of the blue and orange variety, and the dragons, who clearly do have morals, and are counted as allies, but whose reasoning does not always make sense to humans. (Irene met a dragon while trying to steal a book from him — he complimented her on her taste in literature and let her go.) The librarians themselves have unusual moral priorities, as their only goal seems to be to collect books, sometimes saving them from dying parallel universes, without using their supernatural powers to change the world for the better.
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."
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.
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 ship into giving up the curenote by saying they'll cut the communications link to Jupiter - the individual Jovian isn't important to the Hive Mind, but the experiment is. On the other hand, the cure turns out to do more than just cure the Jupiter Plague.
Journey to Chaos: For the trickster god Remho, provoking city-wide panic and confusion is not evil but Enforced Method Acting because it engages the production's extras (i.e. Innocent Bystanders) like nothing else can. Regardless of danger, it draws out that true emotion that leads to excellent performances.
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.
Human telepaths see entering minds without permission as a violation. Dragons, which use telepathy on a daily basis, don’t 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 cow in a pasture as prey waiting to be killed, not someone else's property (when killed, it becomes the killer's).
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.
Dragons have a different concept of time because of their longevity.
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.
This also applies to the aliens in the book. The Martians have no qualms about eliminating the Second Men because they are a collective intelligence with no idea that an individual can even be sentient. The Venusians on the other hand are so mindlessly aggressive that the Fifth Men reach the conclusion that sharing the planet with them is impossible.
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.
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 Yxtrang also have a very codified caste and honor system—to 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."
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 Spider-wolves look ugly as sin but their ships and formations are a thing of beauty, and they don't mind helping humans.
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.
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.
So they cannot sin - sin is an evil done willfully, knowing that it is bad.
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).
Annie Wilkes of Misery thinks nothing of murder and torture, but profanity is one of her Berserk Buttons.
The sphinxes who guard the first gate are inexplicable. 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 without telling him its true purpose.
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 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.
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.
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.
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 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.
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.
Schooled: Capricornhippie lifestyle has left with zero concept of things like private property, licenses, and finance. And he has an unusual amount of patience.
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.
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.
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, these are different 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 (due to events beyond his control) 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.
Lampshaded in Have Space Suit – Will Travel. Kip is trying to understand what crime humanity is being tried for, until the "judge" explains that it isn't a court of justice; because the membership of the Three Galaxies is made up of so many very different species, which all have their own concept of justice or none at all, there can be no one applicable standard. With this in mind, they simply have formed an alliance for mutual protection. The trial is, in fact, to determine if humans are a threat to them.
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.
Second Apocalypse series. The Dunyain monks have a very alien concept of morality. The goal of their order 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.
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 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.
One of the short stories in Skulduggery Pleasant: Armageddon Out of here describes a clan of cannibals who have come to see cannibalism as a perfectly natural part of life for both the prey and the predator - one of the cannibal who appears to be a Token Heroic Orc offers to help Valkyrie when she is caught and being prepared to be cooked. When she gratefully accepts his offer, expecting him to untie her, he begins singing. When she finally manages to make him stop, he explains that he's trying to make her stop thinking about the fact that they're going to eat her, and is horrified when she asks him to untie her instead. He then claims she is not a good friend, because she yells at him, while he is a good friend, because he sings to her.
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 Star Trek: Destiny, the Caeliar's system of absolute pacifism is oft decried by other humanoids as 'imponderable moral calculus.'
In The Traitor Son Cycle, one of the main reasons of the conflict between Men and Wild is this trope. A creature of the Wild believes that once they've beaten something, it's only natural to eat it, even if it was sentient and/or a member of their species. They also have no law beyond "the most powerful of us dictates what we can do", and believe that the only owner of the land is the one who's originally lived there, which is why humans see them as dangerous animals, while the Wild sees humans as greedy and byzantine.
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 Tripods series the eponymous race, while evil from the human heroes' perspective, has its own alien motivations.
During his enslavement, Will learns that using human slaves is a thorny political issue among the Masters and and that some of his master's friends disapprove. However, this is not because of a moral objection to slavery or any concern for the dignity of the enslaved (they have neither). Instead it's merely an economic concern about over-dependence on cheap alien labor.
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. Those people look evil, let's destroy them.
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.
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 Things, the Hugo-nominated short story by Peter Watts, views the events of the 1982 sci-fi horror movie The Thing (1982) from the alien's POV. Every species the Thing has encountered thus far is capable of shapeshifting and merging with other cells just like the Thing, which cannot understand why this strange new 'world' violently resists its attempts to 'commune' and adapt its offshoots (people). On eventually realising the nature of humanity — each offshoot an individual 'thing', isolated and doomed to decay and death — the horrified alien realises it has a duty to infiltrate humanity and bring about its 'evolution' by force.
The eponymous eldrae of the Eldraeverse have one of these arising from their different instinct-set. Sometimes it gets to the same place via different paths. (Example: They would argue that having to fall back on enlightened self-interest to cooperate and build societies is better than instinctual tribalism, because it doesn't come bundled with xenophobia and an instinct to punish defectors from the group norm.) Sometimes, on the other hand, it really doesn't. (Example: They find charity, whether giving or receiving, instinctively repulsive because it's an inherently unbalanced exchange.)
While the book itself only shows relatively minor examples (extreme xenophobia of various strains and problems with comprehending the concept of personal face-to-face relationships, as an example), the possibility of this is a key plot point in Foundation and Earth — the driving question behind the plot is Golan Trevize asking himself why his intuition pointed to Gaia as the most correct option of the three given of First Foundation, Second Foundation, Gaia. At the end of the book, he realizes that the possibility of this trope is the reason — the First Foundation was out at least partly for other reasons, but the Second Foundation was excluded because their entire system is centred around psycho-history — which, among other implicit assumptions, assumes that the populations involved are human populations acting in a human manner, and hence would be incapable of handling truly alien ways of thinking.
In Harahpin, Thrym is unique among Pairetorians as he actually wants to feel pain and suffering. He believes that being denied this is a treacherous thing and means he's not really free. He tells this straight in Xepysa's face.
In Dora Wilk Series, Anubis mummifies his dates so that they may stay with him forever and considers this to be the expression of true love.
Hannibal Lecter's personal ethics are bizarre. Murder, torture, cannibalism and mutilation are fine, but sexual assault and rudeness are punishable by death. What Lecter considers to be rude behaviour is unclear as he himself insults, ignores and talks down to people. And murder could be seen as being pretty rude as well. Furthermore, his definition of evil is to defy the rules of society and he made the deliberate choice to be evil by rejecting societal norms.
The Aing-Tii from the Star Wars Legends Franchise fit this trope to a T. Their technology is quite unlike that of the rest of the galaxy. They are intensely reclusive and xenophobic to the point that they actively try to keep other races from knowing about them, yet they detest slavery to the point that they will attack slave transports and liberate the captives. Not only do they look a little like arthropodic Starfish Aliens. However, what really makes them fit this trope is that see the Force as not just divided between a Dark and Light but many additional colors along the spectrum. This perspective has given their monks access to unique force powers. They are essentially the Mantis Shrimp of force users and the the squid to the Jedi's angels and the Sith's devils.
In Dust of Dreams, the ninth book of the Malazan Book of the Fallen, the K'Chain Che'Malle finally get their own narratives and are shown — as could be expected from telepathically communicating intelligent dinosaurs — to have rather different moral perceptions from humans. They believe in the "logic of despair" and that an existence without an opposing force, without tension, untouched by chaos, is also without meaning, and that freedom lies only in never being certain of one thing only, while for much of the series it has been shown that humans prefer certainty, which for the K'Chain Che'Malle is amoral.
The dragons in the Realm of the Elderlings series perceive the world completely different than humans do. For dragons, they are the kings and queens of the world, and the world and everything in it exists only to make sure the dragons are doing well. It is impossible to make a dragon understand that humans have different priorities, so that the humans have to resort to offering the dragons bargains which benefit the latter to get them to do something not of their immediate concern.
In Karl Schroeder's Permanence this is the case with all known alien races past and present both in relation to humanity and in relation to each other as well, making inter-species communication and cooperation impossible. Thus the story is kicked off by the discovery of a derelict alien ship in which several species seem to have cohabited.
The Lord of Storms in The Spirit Thief, being created for the purpose of hunting demons, prioritizes this over anything else, including world-shattering events, wars and massive collateral damage. It actually takes his (human) deputy several hours to persuade him not to trigger a demon in the middle of a heavily-populated city.
In Verner Vinge's A Deepness in the Sky, Spiders normally conceive children in the Waning years before hibernation and give birth soon after its over. Reproducing "out-of-phase" is considered a perversion, and those born out-of-phase(identifiable by their age) are the subject of a deep-seated stigma. Conservative groups see them as an abomination, and even liberal spiders may have to overcome a knee-jerk aversion to the sight of an out-of-phase child.