The Old World of Darkness features a detailed description of a great many moralities of vampires in a supplement named Chaining The Beast. One believes that suffering is good and if you deprive someone of it you might as well kill them because they won't be strong enough to face life. Another believes that everything must change or die and thus encouraging change is the only good thing you can do.
Most characters (including non-vampires) in Vampire: The Masquerade have three Virtues — Conscience, Self-Control and Courage. On the alternate paths of Morality, vampires often switch out Conscience and Self-Control with Conviction and Instinct. Not only do they no longer see virtue in human terms, they don't see it in other supernaturals' terms. (Old world mechanics were not designed to work across venues.)
These paths are a favorite of the Sabbat (who believe they are better than humanity, and deserve to rule over them) and the Independent clans. Such alternate paths include the Path of Night (favored by the Lasombra), which penalizes them for helping others or repenting for one's actions; the Path of Metamorphosis (favored by the Tzimisce), which focuses on understanding change in the most disgusting ways possible; the Path of Paradox (favored by the Ravnos), which holds to an extreme version of Indian conceptions of reincarnation and dharma in which one must manipulate and deceive others into following their svadharma — while killing non-Paradox vampires who exist outside the cycle without contributing to it; and the Path of Lilith, which teaches that wisdom comes through suffering, so suffering must be good (in moderation).
There's exactly one Path in the 20th Anniversary Edition that doesn't fall under this. The Path of Honorable Accord is heavily based on codes of honorable conduct such as chivalry or bushido, and although a follower is not humane (indeed, they usually see humans as chattel, or at best as creatures who are admirable in their own way, but inherently inferior, like a hunting hound or warhorse) or pleasant to be around, most people would recognize them as a moral being following a comprehensible code. As such, it's the only one listed that doesn't use either of the alternate virtues.
In Dark Ages: Vampire, there are five major Roads of vampiric morality: the Road of the Beast, the Road of Heaven, the Road of Humanity, the Road of Kings, and the Road of Sin. All of them, being ways to keep the Beast in check, differ from human expectations - even Humanity, which expects you to be a better human than some actual humans.
The Kuei-jin, the Kindred of the East, are a different kind of vampire altogether, being damned escapees from the Thousand Hells. They pursue Dharmas, paths to enlightenment, and most Dharmas don't resemble mortal moralities in the least - one expects you to be the greatest devil you can, one expects you to create, live through, and destroy a succession of mortal identities, and another claims you're a reincarnated god and must reclaim your divine identity. The closest to a human perspective, the Flame of the Rising Phoenix, seeks to settle the dues of their mortal lives and live as a human would, encourage others to appreciate the value of humanity and experience, and resist the inner demon.
Mage: The Ascension makes this a part of the mechanics (such as they are) of the game's magic system. For example: Playing a Euthanatos mage might mean that you need to kill a bunch of people at certain times and certain places in order to keep the world balanced and working properly. As a Cultist of Ecstasy, you might need to do a lot of drugs and sleep with a lot of people in order to transcend your limitations. Even if you're not playing a stereotype of the Traditions, your Avatar might have a wholly different outlook on the world from its host and may not work properly for the mage unless he/she brings his/her perspective more in line with the Avatar's.
In the New World of Darkness, the base humanKarma Meter is called Morality. All supernaturals have their own uniquely named Karma Meter, which has slightly different purposes for them. For most of them, these meters ultimately are identical to human moral behavior, simply adding unique sins and crimes that aren't an option for a mortal but make sense in human terms (e.g. magical compulsion of a sentient being for a mage). Some, however, are more alien...
Werewolves have Harmony, how in tune they are with themselves. Since they're half spirit and part wolf, killing humans isn't even a blip on their conscience unless it was just done for the hell of it. Being disloyal to their pack is far more troubling than even pointless murder of humans.
Other human sins like stealing are also notably absent, but as spirits elements of etiquette frequently take their place. EATING a human is forbidden but only because it dishonors half of your heritage, and being impolite to a social superior is a sin that can result in so much inner guilt and conflict that it can literally drive you insane.
Sin-Eaters have Synergy, measuring how in tune the Sin-Eater is with their geist, and with the balance between life and death. Deliberate killing is absolutely no problem for a Sin-Eater, emblematic of 'clean' death, but serial killing and mass murder are seriously disruptive, emblematic of 'unclean' death, while any means of attempting to resuscitate a dying person plays havoc with the balance of life and death. And attempted suicide will piss your geist right off.
And accidentally killing someone is a no-no, as well. If you meant to, no problem.
Hunters can inflict this on themselves with the optional rules for setting up a hunter's code. One provided example ends up with a personal duty to kill every mage she meets, lest she suffer the same psychological effect as a normal person would get for accidentally murdering someone.
Demons have extremely alien morality, such that they can reverse Vices and Virtues; Generosity becomes a sin because it endangers the demon's life or sacrifices resources he and/or his friends need, whilst Pride is good because it helps him assert his self-will and inherent right to be a free entity.
For The God-Machine Chronicle, the Morality system was overhauled, going from a Karma Meter to a Sanity Meter. The Morality trait was renamed Integrity, and the list of sins was removed; it now handles how well ordinary people deal with events they can't rationalize or cope with.
The True Fae are most definitely this. They come from a world of utter chaos where everyone must strike their own stake to avoid fading into oblivion; ergo, their lives are consumed by conflict and the eternal struggle for more glory. They adopt emotions as passing fancies, but don't understand them; the book cites a True Fae falling in love with a changeling, only to snap his neck when he hesitates to pass the salt and recalling the burbling of a brook in summer when it hears the changeling's dying gurgles. This is NICE for a True Fae. You really, really, really, really, really, really, really, really, really, really don't want to know what "Nasty" is. Oh, and if they ever try to understand humanity, they lose most of their power and all of their memories of Faerie.
As with the True Fae, Spirits have inherently alien morality; they are not human, never were human, and even the most intelligent of all spirits are fundamentally alien beings. The closest one can get to defining a spirit's morality is the basic assumption "promotes my area of influence = good" and "denies my area of influence = bad". Plus whatever unique character quirks of motivation and Ban (a forbidden action, literally the closest thing a spirit has to an unforgiveable sin) drive a given spirit. This is why spirits can never truly be reasoned with, and certainly not trusted; a fire spirit has to burn things, and simply cannot care about anyone it maims or kills; all that matters to it is that things were burnt, and the idea of caring about the fuel-source is incomprehensible. Meanwhile, a spirit of love may well force someone who is experiencing Domestic Abuse to stay with their abuser, simply because "they still love each other", and thusly the pain the abuser inflicts is unimportant compared to the diminishing of love that would be caused by separating them. This is why there are no "Good Guy" Spirits, and some of the most innocuous seeming spirits are actually some of the most dangerous — playground spirits, in particular, tend to be monsters fed on a diet of intense conflict, sorrow and cruelty, thus actively promoting or sheltering everything from common bullies to pedophiles and other child molesters.
In the fanlines, Geniuses have Obligation, which is more along the lines of how in-tune they are with the rest of humanity. The lower it dips, or the more powerful the Genius gets, the more likely they are to drift toward Blue And Orange Morality. When that happens, they tend to start viewing people more as collections of spare parts.
In Exalted, The Fair Folk fall into this; at base, the unshaped (and many shaped) raksha simply have trouble comprehending that anyone else is a separate being that might not care about their agenda, and they don't see why humans are so afraid of the chaotic madness of the Wyld. Those who do comprehend humanity still tend to subscribe to alien (read: soul-eatingly dangerous) morality, but there are exceptions.Graceful Wicked Masques puts it best:
All other characters in the Exalted setting are unique beings with their own unique Motivations, personalities and memories. A raksha is not a being like that — not really. Instead, a raksha is actually an incoherent and incomprehensible mass of seething chaos that — for some impenetrable reason of its own — pretends to be a unique being with its Motivation, personality and memories. The first step in understanding and creating a raksha character is to understand that everything about that character is a deception engineered to facilitate an interaction between a shaped being of Creation and an entity so far removed from Creation as to be utterly beyond mortal comprehension.
A similar deal goes with many of the Primordials. They are, at their very core, pure, undefiled concepts, which means they have trouble understanding anything outside their purview. She Who Lives in Her Name honestly thinks everyone would be better as mindless pieces in a hierarchical machine, the Ebon Dragon can't understand why anyone would do something that doesn't hurt someone else (unless they're setting up for the inevitable betrayal), and Autochthon views innate progress and innovation as awesomesauce but can't possibly foresee the consequences. Adorjan has a particularly impressive case, since she's redefined her Compassion so that killing someone in an agonisingly painful fashion is, to her, a compassionate act because they're so quiet afterwards and silence is the greatest gift.
Nobilisthrives on this trope, particularly in the sidebar "microfiction" vignettes. While the Nobles have an ultimately good goal (they want to save the universe), some want to destroy humanity as well. The Nobilis, even the more traditional "good guy" types, see things in a different way than you or me. They are, after all, living personifications of concepts. And then there are the Excrucians, who have a morality that freaks out the Nobilis. Yipe.
In Kult, reality itself is an illusion, and the true reality behind it is very different. Any character who knows anything about the truth and acts on this knowledge rather then just playing normal will be perceived as insane at best. One basic rule is that you need to achieve as extreme a mental balance as possible in order to break free from the illusion. A normal person has a mental balance of zero, the weakest and most vulnerable position possible. Thus, helping people with negative mental balance climbing back up to zero is actually doing them a disfavor, unless you can keep pushing them upwards to high levels of positive mental balance. This means that it's usually a bad thing to heal a trauma or cure a mental disorder. It also means that any person with negative mental balance (or positive balance very close to zero) potentially has a lot to gain from getting tortured, raped, or even murdered. Positive mental balance is even more alien, although much neater.
Some source material from Paranoia suggests that Friend Computer works on this system. Either that, or its goals are just really screwy. No one can be quite sure, and trying to be is treason.
Ogres have almost no concept of morality beyond Might Makes Right. In their culture, iron is more valuable than gold, because with a bag of gold, you can buy an iron weapon and lose the gold, but with an iron weapon, you can kill someone and take their gold and keep the weapon. Eating is pretty much their shtick, to the point where their religion revolves around it; they worship a being called the Great Maw, which is the personification of hunger, and to advance in society, you have to kill and devour the Ogre above you. Their females view a particularly large paunch as the most attractive trait in a male, and they view disembowelment as the absolute worst way to die (in fact, one of them, Bragg, is The Dreaded among their kind because disembowelment is his favoured method of execution).
The Dwarves of this setting are obsessed by Revenge Before Reason, to the point of Too Dumb to Live territory. They never forgive and never forget, no matter how trivial the slight, and grudges have set conditions for fulfillment, usually disproportionately high. When they're fulfilled, the matter is settled, with the Dwarves abandoning the conflict halfway through and returning home secure of their success. Case in point: they once went to a war against a human lord and slaughtered his men by the hundreds because six years ago, when Dwarven workers were building his castle, he underpaid by twelve pennies. They also take the casualties from their vengeance-seeking campaigns and place them in the Book of Grudges as grudges to be paid back later. This all means that Dwarves are in a near-constant state of war with everyone and can't breed fast enough to make up the losses. They also really love their beards. Shaving them is a dire insult. One of the old Elven kings shaved the beard of a Dwarf emissary, which resulted inElves Versus Dwarves on the scale of a Guilt-Free Extermination War. When the Dwarves finally killed the offending king they kept his crown in lieu of the Elves paying their expenses for the war and otherwise called it settled.
Da Orks were created by long-dead Precursors as Living Weapons, and so enthusiastically wageWAAAGH!!! on anyone they encounter, or failing that, other Orks. They don't understand morality; for Orks the only limits are what their boss lets them get away with. Orks don't understand friendship, but some have "favourite enemies". And they don't understand that other races might prefer not to fight; why would you build a big killy fortress in the first place if you weren't hoping that someone would come along and attack it? Endless war for the sake of war is all the Orks know how to do. This mentality is in part due to them being genetically engineered for war, and because they were late to the party when the Nightbringer hammered the fear of death into all other sapient species.
To most races including humans, decapitating a defeated enemy, sticking the head onto the end of a sharpened stake and wearing it on your back into battles is desecration of the dead and an act of supreme barbarity. To an Ork, doing this is a mark of respect to the defeated opponent.
The Tau qualify due to their devotion to the Greater Good. The Ciaphas Cain novel For The Emperor spends a bit of time on this, stating that any action that goes contrary to the Greater Good is detested almost to a physical reaction, and Tau can't understand why others would willfully refuse to follow it. Also, several Tau belief systems are contrary to the Imperium's: Tau have little to no individuality, view personal ambition to be the greatest of sins, and consider Last Stands to be foolish (if the top brass ordered it) or an ordinary sacrifice (if the foot soldiers are resorting to it) rather than heroic.
The Dark Eldar as well, when they aren't outright evil. They see absolutely nothing wrong with brutally torturing, raping and killing people for their gratification. They greatly enjoy being tortured themselves, but they think being bored in a locked room with nothing to do is a Fate Worse than Death. For this reason, Dark Eldar are often punished by being forced into Commorragh's factories and slave pits, where they find little to stimulate them. Also, as Andy Chambers' Path of the Dark Eldar series shows, they have a sense of personal honour, if a very perverse and twisted one, and it doesn't apply to anyone who isn't an Eldar.
All of the Chaos gods fall into this. They do what they do because they are made from that thing, and exist to propagate the ideology that they feed on. While they're the 'verse's Ultimate Evils, the fact that they're also fed by positive emotions such as honor or hope adds some twisted nuance.
Khorne offers his followers incredible strength and determination, asking for nothing more than spilt blood and skulls offered in his name; from your enemies, from your friends, from you, he's not picky. That said, Khorne also has a martial code of sorts, and despises cowards who flee from battle or who use magic to win. In some accounts he even rejects bloody offerings made from defenseless noncombatants, or favors those who kill with melee weapons over those who use heavy ordnance.
Tzeentch is often praised as the greatest Chessmaster in existence, but this is a misconception. Tzeentch has no great end goal, and doesn't particularly care if his plans succeed or fail; as an incarnation of ambition and change, were he ever to win, there would be nothing to scheme against. To this end, Tzeentch deliberately sets up his plots to crash into each other, and while he's willing to grant his followers a portion of his arcane might and intellect, he's just as likely to bless them with a mutation or two. Or twenty.
Nurgle loves life, and wants to cram as much of it into the universe as he can; unfortunately this includes bacteria, viruses, and diseases. His idea of affection is to bless you with some horrible affliction, and considers your misery a form of gratitude. Nurgle is the Chaos God of Despair, yet the most fatherly or avuncular of the Dark Gods, since his followers are so resigned to their gruesome fate that they develop a sense of morbid good humor about their rotting flesh and disease-bloated bodies.
Slaanesh's motivations can be seen as a devotion to sensation, and devotion to devotion itself. His/her followers are granted all the pleasure and excess they desire, be it music, women, food, whatever. Unfortunately a mortal body can only take so much of this, so that Slaanesh's followers eventually become burnt-out husks of men and women forced to partake in increasingly exotic and extreme diversions to titillate their jaded senses. They also think that they should offer excess to everyone else, and that is nota goodthing.
The Fair Folk in Halt Evil Doer for Mutants & Masterminds. Convention has it that the Lords of Winter are the "bad guys" and the Lords of Summer the "good guys". Word of God is that convention is completely wrong — it's just that the Lords of Summer happen to be the Anthropomorphic Personification of happy dreams and the Lords of Winter of nightmares. But that doesn't mean the Lords of Summer care about humans, or the Lords of Winter are actively malevolent. (However the current leader of the Lords of Winter is a human villain who is a straight-up bad guy.)
The aurads, in the third-party D&D 3e setting Oathbound, "can accept betrayal if it is explained eloquently, but might take issue at an excellent gift presented without proper ceremony."
In the Dungeons & DragonsMystara campaign setting, the Immortal (D&D's functional equivalent of AD&D's gods) Nyx was definitely this. All the other Immortals of Entropy were just straightforwardly evil. Nyx, on the other hand, loved every living thing in the universe as if they were her own children. It's just that she believed that living things were children who ought to be helped to mature into undead. She wanted to transform the world into one in which the undead would dominate the living. She wasn't evil in the sense of wanting to harm anyone; she genuinely believed that the world would be a better place if more people became vampires, liches, ghosts, or what have you, and if those undead beings ruled the world.
Many True Neutral D&D characters are simply beings whose morality is incomprehensible to us. This becomes even more likely if the entity in question is a god, Eldritch Abomination, or Outsider (that is to say, alien from another dimension), or even just a normal person who has spent a lot of time around any of the above.
In Mystic Empyrean every player is an Eidolon who is defined by a Creed. This creed is a set of 3 rules that the Eidolon swears to uphold at the cost of their very existence, and when they break any of them, their very soul starts to fall apart. Then there are traits, which are facets of an Eidolon's personality given form. In the game, the players have to roleplay these traits to improve them, and as they 'level up' to more and more intense levels, the players are expected to roleplay them more and more. For example, the trait "Weapon For the Strong" is connected to Obedience. An eidolon with this trait starts off being able to change into mundane weapons, but has to obey the one they recognize as their master, later on they get into tank sized and equivalent powered weapons, and can even operate a single function of themselves (like drive the tank or shoot the cannon), but have to obey anybody they see as having legitimate authority over them. At the final levels, they can become city and world destroying space ships, mechs, and legendary weapons of colossal magical power, and can even act independently, but they cannot act at all unless given an order to do so. This obviously gives many Eidolons some very strange morality systems when you combine traits and creeds.
The Champions scenario book The Sands of Time plays with but ultimately averts this trope. Renewal and the Right Hand follow moral principles a little different to those of most heroes, but they are ultimately on the same side. Conversely, Belragor comes from very far outside most PCs' frame of reference, and his allies and followers are frequently just plain weird, and few of them define what they do as "evil", but ultimately his motives are all about uncomplicated greed and ambition.
The Daelkyr from the Eberron setting. They invaded the mortal world several thousand years ago for some reason, wreaked a massive amount of havoc for little apparent benefit, and nobody really understands a thing they've done since. Word of God from setting creator Keith Baker indicates that this is what makes them so frightening and worthy of a place among the setting's top supernatural threats- sure, the Overlords of the Age of Demons are much more powerful, and the quori of the Dreaming Dark are more cunning, better organized, and have more influence, but nobody truly understands the Daelkyr or can predict their next movenote Word of God also indicates that their motivation is being a race of Mad Artists who destroy worlds as a form of bizarre creative expression, which may make them more or less comprehensible.