In the Red Dwarf series and novels, Cats have this compared to humans, which is played for laughs. To humans, Cat comes off as incredibly vain, shallow, easily-distracted, horny, impulsive and silly. To another Cat, he would be quite normal. Although the episode Waiting for God shows that the Cat people have a morality of their own. Because they regard Lister as their god, they consider it virtuous to be slobby like him, and so would regard Cat as immoral because he is cool. In other words, cool = bad and slobby = good in their morality.
In the series episode "Rimmerworld", a world populated entirely by clones and Opposite Sex Clones of Rimmer ends up a fascistic society built around hypocrisy, manipulation, boot-licking, backstabbing, double-dealing, two-facedness and otherwise Jerkass mindsets. Lister, Cat and Kryten are promptly sentenced to death for not only being "hideously deformed", but for being brave, compassionate, loyal, honorable and charismatic, which are all high crimes on Rimmerworld.
Anti-Villain Morgaine in the story "Battlefield" thinks nothing of slaughtering people who tick her off, but insists on paying for a round of drinks that her son ordered in. She pays for them, by the way, by curing the barmaid's blindness. She also won't fight in graveyards as to not dishonor the dead. She also held a ceremony honouring said dead — dead people on a planet she cared nothing of. They died in battle = They deserve honour.
The Doctor himself sometimes borders on this, thinking almost nothing of taking his friends to dangerous places all the time.
The Fourth Doctor is about as extreme as it gets due to the Bizarre Alien Psychology of that incarnation - he sees no problem with manipulating or bullying his friends for the greater good or even, occasionally, for fun, but finds the whole concept of exercising authority over others to be at best objectionable. Sometimes, if it looks like he's led allies to fend off a monster to the point where his allies can gain official power, he will stab them in the back to keep this from happening. The first thing he will offer any villain in a dispute is compromise and diplomacy, no matter how repugnant its ideas - of course, if the villain has no intention to change or betrays him, he will not feel any guilt about killing them.
Another example are the Sontarans. Their entire morality system is based around the glory of battle. They love war and will start one for any reason, and they see dying in battle as the most honorable possible death, thus they have no qualms about killing the enemy in battle. In fact, they will often joke and congratulate their enemies while they are doing well, including killing them all, and will greet people with such sweet nothings as "I hope one day to spill your intestines on the battlefield". But it is morally reprehensible to kill someone who isn't fit for battle while not at war with them; such killing is considered murder. This is really highlighted in "A Good Man Goes to War": one of the biggest punishments for a Sontaran is to become a field medic, because not only are you not fighting, but you're actively stopping people from being able to die a glorious death in battle.
The Cybermen at least started out as having a morality which felt alien to humans, thanks to their emotionless logic. In "The Tenth Planet" they intend to destroy Earth. When one human character screams out that they are killing people, the Cyberman merely points out how illogical her outburst is, as people die all over the world constantly, and the human does not display any distress over that. The Cybermen were not even actively malicious in the story. Their survival simply meant that Earth had to be destroyed, so they set about to do that. They even offered the nearby humans that they could continue their existence as Cybermen, which seemed like a perfectly reasonable proposal to the Cybermen themselves.
The Eternals in the story "Enlightenment": they think nothing of kidnapping human seafarers to crew the ships in their race, and aren't too bothered by their deaths — after all they're outside of time and technically don't die, but "Ephemerals" (beings inside of time) live such short lives. All that matters to them is winning the race and the eventual prize, the "Enlightenment" of the title. They're not even bothered about sabotaging each other's efforts — it's not against the rules, technically, just not terribly sporting.
The Judoon have a pretty strange concept of justice. In "Smith And Jones", they don't hesitate to pronounce and carry out a death sentence on a man for breaking a vase over a soldier's head, even though the soldier was fully armored and completely unharmed, and when the hospital appears about to explode they depart without any effort to stop it. But when their leader takes an unusually long time verifying that Martha is human, he insists on giving her "compensation" in the form of a piece of paper in an alien language (it's never clear what it is), and when the hospital doesn't blow up they send it back to Earth.
This may be more Lawful Stupid, since the whole reason they took the hospital in the first place was to comply with jurisdiction rules.
While the Daleks are mostly Scary Dogmatic Aliens with heavy Nazi overtones, it's noted that they regard hatred as so fundamentally beautiful that they are unable to destroy especially pure examples of it, even when it's in their best interests to do so. It's subtly implied that part of the reason they have not yet defeated the Doctor may be that they're too in awe of the hatred he has of them.
The Ancientsmight be this trope after their ascension. Whenever we see living Ancients on this plane of existence, they are generally depicted as normal humans who were simply interested in science a lot, not the gigantic Jerkasses they are as ascended beings (see more on Neglectful Precursors).
In "Learning Curve", SG-1 encounters a technologically-advanced planet where the human civilization implants nanites into certain children at infancy that records all information they learn. When they come of age, these nanites are removed and distributed to the rest of the population, transferring their knowledge while reducing the children to a largely infantile state. SG-1 is horrified to discover that the children are essentially "having their brains sucked out" but the other civilization seems to have no issue with this.
Cameron of The Sarah Connor Chronicles has a very simple morality system that revolves around protecting John Connor. If it protects him, she'll usually do it, unless he overrides her (most of the time). If it threatens John Connor, however, she destroys it without hesitation, and regardless of whether John or anyone else objects. That's pretty much the beginning and the end of her concept of morality.
Worth noting is early in the first season, Cameron guns down a FBI informant in front of Sarah for warning the FBI about the Connors, and Sarah slaps her in response, telling her never to do that again. Cameron's response is to stare at her in absolute but emotionless confusion; after all, Cameron just did everything right by her programming, but Sarah's telling her she did the wrong thing.
Another example of this occurs later, when Cameron uses a man on the run from the mob to get information on who the Turk prototype computer was sold to. She promises to help the man, but the moment she has the information, she simply walks away and lets the mob hitmen kill him. For a human character, this would be an act of cruelty that — depending on the character — could catapult them over the Moral Event Horizon, but for Cameron, the audience knows that her morality system is extremely alien compared to a human's, and thus the result isn't as severe; the audience is just reminded that Cameron is still a machine assassin and still coldly and brutally logical about her mission.
Present-day John and Sarah invented the 'stop Skynet' mission, so they're able to define how that mission operates, including setting limits on killing people who might interfere with that mission. (This is compared to the 'protect John' mission, which they cannot interfere with...Cameron will do anything to protect him, period, regardless of what he wants.) However, John never ordered her to not put people in danger or to help them escape danger, just to not kill them.
At one point, when John is surprised that a Terminator isn't cruel for cruelty's sake, Cameron points out to him that terminators aren't cruel. This applies to both Cameron herself and "evil" terminators in general, who, while utterly ruthless, don't inflict pain just for the sake of inflicting pain. While they are willing to torture humans (not usually for interrogation, but for other purposes, like hurting someone's loved ones to draw them out of hiding), the moment they determine that this will not achieve their goals they stop and utilize other tactics.
A sideplot in Babylon 5 episode "Geometry of Shadows" revolves around Ivanova trying to understand Drazi politics before the conflict between Purple and Green spirals out of control. Aside from colors, Purple and Green are wholly abstract concepts with no defining characteristics like ideology or regional identity. Drazi foreign policy is quite understandable by humans, though.
The Vorlons and Shadows initially appear to be Good Is Not Nice and Always Chaotic Evil, respectively. But really they're Lawful Blue and Chaotic Orange, essentially using the younger races as arguments in a million years-old philosophy debate on the nature of Order Versus Chaos.
The Borg in Star Trek: The Next Generation were a lot like this originally, before eventually being humanized by the addition of the Borg Queen in the movie First Contact.
Locutus: "Why do you resist? We only wish to raise the quality of life."
The entity Nagilum in the episode "Where Silence Has Lease" traps the Enterprise in a strange Negative Space Wedgie, kills a Redshirt, and decides to kill a good portion of the rest of the crew to fully explore the concept of death. It seems to truly have no idea that the crew might not be wild about this idea.
In one fanfic, there was a discussion of Q vs. Nagilum among the core cast—who would you rather deal with? The conclusion was Q, because in his own odd way he seemed to like humans in general and the "Enterprise" crew in particular, while Nagilum seemed to be indifferent to anything but the results of his experiments.
In the episode "Liaisons", had ambassadors from a race that lacked the concepts of antagonism, pleasure and love. One of them studied antagonism by being a jerk to Worf, one of them studied pleasure by pigging out, and one of them tried to learn about love by stranding Picard on a planet and taking the form of a human woman.
While Q is portrayed as being an adversary of humanity, he might embody this trope. In the episode "True Q", he even claims his race has the right to decide whether humans live or die because of their superior morality, a characterization with which Picard disagrees, to put it mildly.
Although Q is a particularly malicious member of his race. While the Q Continuum do fall under this Trope, Q himself is particularly sadistic and condescending compared to the others, and isn't the best comparison for how his species thinks (the Continuum once kicked him out and turned him into a human for being an embarrassment).
Malicious perhaps, though it's not hard to make the case that every time Q shows up (on TNG anyway), he does the human race a favor - even if it's a lesson or warning that costs lives. He really seems to like humanity, but is happy to make liking him back nearly impossible. Which makes him perfect for this page.
In the final episode he actually saved humanity indirectly by dropping hints about what the continuum was doing so that Picard could stop it. In an earlier episode where he was acting as their agent he admitted the Q as a whole considered humans a possible future threat.
In the extended canon novel Q&A it is revealed that Q's tests had a point all along... turning Q into a case of Values Dissonance. A race known as Them have returned to decide the fate of the entire universe. It turns out They created our universe (the Q included) and, like many others they created before ours, They are now going to destroy it... because They are no longer entertained by it. The Q knew all along and had essentially given up. Q, however, (yes that one) had tested countless races and decided on Humans, Picard in particular, to prove the worth of keeping our universe around. It works. Picard convinces Them to let the universe remain... by laughing at the absurdity of the situation. All along Q had been teaching Picard to have a sense of humor about things that were out of his control just so he would have exactly this reaction when the time came.
And then you begin to realize that the fans of Star Trek are essentially Them... what with the recent drastic decline in the franchise's popularity. EPIC!
In the episode "Allegiance," Picard is whisked away to a strange prison with three strangers and replaced by a doppelganger on the Enterprise. When he figures out the experiment he and the others have been unwittingly participating in, his captors (a group of previously unknown aliens) reveal themselves and return him to his ship. They explain that they sought to understand command structures, which do not exist in their culture. When Picard tells them that what they've done is wrong, they claim not to understand the "primitive" concept of morality. But it's clear, when Picard gives them a taste of their own medicine, that he doesn't entirely buy their alleged Blue And Orange Morality, and that maybe they're just assholes.
Another example is the Klingon concept of honor, which doesn't track exactly to any human honor system. For instance, hiding in a debris field to ambush anyone who comes to rescue survivors is considered perfectly honorable, and you can officially strip someone of honor for political reasons. Worf is unusual in that his honor is a code of behavior understandable by humans, more like a Knight Errant than anything, but it confuses the hell out of other Klingons.
Note that Worf's code of honor is TECHNICALLY the same as the other Klingons, the difference being that he stands by it while other Klingons often tend to interpret the 'honorable' thing as being 'the thing that gains them glory.' The other Klingons he encounters tend to believe that he will also do what serves himself first, then get surprised and offended when he declares that he will follow through with his promises and oaths.
Fridge brilliance to be found here: Worf was raised on a human colony (and later Earth). Even though he's well read in the facts of what constitute honourable and dishonourable acts for a Klingon, he has very little firsthand experience with the Klingon expression of it (where it's practically EXP), and instead expresses it like a human (a state of mind).
In the episode "Suddenly Human", the Enterprise crew discovers a human teenager amongst a group of stranded Talarian teenagers. They soon learn that he was the son of a Starfleet officer who died in a Talarian attack, the Talarian captain took him in as his son since according to Talarian tradition, he is allowed to claim the son of a slain enemy after he lost his own son in a Starfleet attack.
In Star Trek: The Original Series the non-humanoid Excalbian race provides another example; they view such concepts as "good" and "evil" as being so foreign that they decide to test them experimentally by staging a battle between representatives of the two.
In the episode "Empath," the aliens torture the Enterprise officers in order to awaken the title character's compassion.
In Star Trek: Deep Space Nine The episode "Captive Pursuit" was all about this trope. The first alien from the other side of the wormhole, who calls himself Tosk, makes friends with O'Brien and is revealed to be the prey of another species, and both that species and Tosk view the hunt involved to be ancient and honorable for all involved. Tosk even refuses asylum on DS9, even though he will be turned into a zoo exhibit for the rest of his days, the most dishonorable outcome of the hunt. O'Brien is especially troubled by this, and actually subverts the trope a bit by making a compromise between the two moralities: he frees Tosk so that he and his pursuers can have the hunt they desire, and so that Tosk has an opportunity to live the way he deems most honorable, all while allaying O'Brien's conscience about Tosk's fate.
The Cardassians, specifically their justice system, where the verdict is announced before the trial begins. The trial only happens to explain why and how the crime was accomplished and justify the initial verdict. The system is justified by the Cardassian's attention to detail and their perception that they cannot make a mistake (although it is proven wrong in Star Trek multiple times). This extends to all aspects of Cardassian culture, with "Enigma" (mystery) novels always end with everyone being guilty: the mystery lying in who is guilty of what. Starfleet people are shown to be unable to understand that system.
The Ferengi have their own concept of right and wrong, which is closely related to what is profitable and what isn't. Their whole value system is related to profit and greed (which is seen as "the purest feeling"). Again, Starfleet people are shown to be unable to comprehend the Ferengi and their morality, feeling superior to them because Starfleet morality is all about being generous, peaceful and impartial.
The Mari, a one-episode race in Star Trek: Voyager, are telepaths who prosecute thoughtcrime. However, they are in no way fascist (indeed, the laws have made the police almost obsolete and there are very few left) and the head constable is genuinely trying to do the right thing. While their laws are draconian and lead to the episode's problems, the fact that they have laws regulating thoughts is presented as a logical consequence of a telepathic society.
The Hirogen. They are a race of hunters, only they have no problem hunting sentient beings (and sometimes eating them) and do it as a way of life. Though they have a moral code about respecting difficult prey and are perfectly willing to hunt prey that doesn't have to be killed or can be revived, as long as they prove to be a challenge.
An early episode of Star Trek: Enterprise had the crew being continually attacked by a mystery ship for no apparent reason. T'Pol points out that not every species out there necessarily behaves in a way that would make sense to humans. They never find out what the aliens' motivation was, but they did successfully test their new weapons on them.
A little more elaboration: the Addamses possess a clear taste for the grotesque and the macabre, and a distaste for the opposite. Their house is a sentient haunted house, they wear dark clothing, the children routinely torture each other for fun, and find monstrously hideous creatures to be adorable. On the flip-side, they react to cute and cheery things like songbirds, kittens and flowers to the point of physical revulsion. That said, they aren't really "evil", and in fact they're rather courteous (in a twisted sorta way) to outsiders, although they do consider us to be the strange ones.
Played for (ironic) horror in the sequel to The Movie, Addams Family Values(the title says it all, doesn't it?), when Gomez and Morticia's infant son contracts a disease that turns him from a pale-skinned, mustachioed mutant into a stereotypically cute, fully human baby with a healthy complexion and curly blond hair. Granny tells the parents that the condition might be incurable.
Granny: He could stay this way for years, perhaps forever...He could become a lawyer...An orthodontist...President.
[Gomez screams in anguish.]
The Munsters, meanwhile, possessed a similar mentality. However, there was a key difference: the Addams Family were humans who acted like monsters, whereas the Munsters, as their name suggests, were clearly inhuman, but acted like normal people. It made for an interesting contrast.
The Head Six and Head Baltar entities of Battlestar Galactica. Ron Moore says that their kind are the inspiration for stories of angels and stories of demons. It's not hard to believe.
Witness the huge discussion on the Headscratchers page over what Jasmine's hypothetical "alignment" was. Sure, she brings total peace and happiness to the world, but she eats people (but usually no more than one or two a day, far fewer than would be killed by wars and crimes her presence would prevent), and people have no choice but to love and adore her. Can any human definition of "good" or "evil" really describe her? (That was rhetorical, by the way)
Present in an early episode, "Bachelor Party", with a family of Ano-Movic. Ano-Movic demons are a very peaceful race — formerly a violent race of nomadic demons, they blended into Western Society and gave up their more gruesome traditions. On the flip side, not all of their old customs have been abandoned — the family seen in the episode are shown discussing the wedding plans just as easily as they discuss the ritualistic eating of the former spouse's brains. While this sounds gruesome, to the Ano-Movics, it is a gesture of love — their belief is that by eating the brains of the old spouse of their wedded-to-be prior to the wedding, the new spouse will incorporate all of the love and affection from the previous relationship into their new marriage.
Illyria demonstrates this to a large extent, and due to being in a human body she, partly against her will, starts to feel human emotions and assimilate human values. When Wesley betrays her she's perturbed at the fact that it bothers her, as "betrayal was a neutral word in my day. As unjudged a word as water or breeze". She spends quite a lot of time trying to figure out why mortals act as they do. She describes her world view quite well to Angel:
"I didn't give you a chance. That you learn when you become a King. You learn to destroy everything that isn't utterly yours. All that matters is victory. That's how your reign persists. You are a slave to an insane construct. You are moral. A true ruler is as moral as a hurricane, empty but for the force of his gale. But you; trapped in the web of the Wolf, the Ram, the Hart. So much power here! And you quibble at its price. If you want to win a war, you must serve no master but your own ambition."
The Observers from Mystery Science Theater 3000 get a little of this, being brains in pans who have evolved beyond the need for physical bodies (even if their brains still need to be carried around by their former bodies). Though in truth it seems more like they're just jerks who pretend like they have their own moral code to justify being jerks. Brain Guy himself explains why he serves as a medic rather than a combatant during a battle as follows.
"My species is a race of pacifists, we only believe in killing out of personal spite."
The Bots also have this. Thanks to Joel programming them with "occasional ribbing," it makes them believe it is okay for them to destroy Mike\Joel's prized possessions, but when someone messes with their things it's Serious Business.
The Plokavians in Farscape. Because they all have a perfectly Photographic Memory, they consider subjectivity and personal colouring of experiences to be alien concepts; so, when each of Moya's crew gives a slightly different testimony of the destruction of a Plokavian merchant ship by Talyn, the judges accuse them of lying. Eventually, Crichton manages to placate them (for a time) by claiming that they were lying in defence of each other, a concept that the judges are more familiar with.
Gosei Knight in Tensou Sentai Goseiger believes in protecting the Earth, much as the Gosei Angels do. However, their definition extends to all life forms on it, whereas his definition applies strictly to the Earth itself.
The Observers from Fringe. It's almost certain that they have some system of logic and morality guiding their decisions, but since they basically exist outside of time and their perspective on events is almost as impossible to understand as their writing, working out what's going on in their pale and hairless heads is...well, something nobody human has managed to do with complete accuracy yet.
It has been shown that they feel morally obligated to "repair" the timeline when they inadvertently prevent a foreseen event from occurring. Although it remains to be seen whether that's a moral obligation or if they're just doing their job.
Their driving motivations so far appear to be ensuring that events happen as they were meant to happen, and "important" people are kept safe.
That's the Observer science team. The ones known in season 5 as the Invaders are primarily concerned with preserving their own Vichy Earth.
In The Big Bang Theory, Sheldon Cooper has a mindset that cannot be easily understood by other people. Usually people around him consider him as mean and selfish, but when Penny ran out of money and asked him for help, Sheldon took out his savings and wanted to lend her much more than she would have thought about. An interpretation is that Sheldon is not really selfish, but he has a different standard of "good" behavior. Alternatively, this may be because he did not actually care about the money. As he said, it was money he wasn't using and did not expect to use anytime soon.
Sheldon has a "this is fact" and "this is not fact" mindset. Usually, the way he sees things, "it is a fact" that he is intellectually superior, therefore deserving of more praise and acknowledgement. Similarly, upon seeing Penny in financial hardship, he recognized the fact that he had more money than he needed, whereas Penny needed more money than she had, and therefore the right thing to do was lend her money.
The show seems to implicitly recognize that Sheldon is not just a crazy person, and that there is some alien logic behind his actions. It gets a rather appropriate Lampshade Hanging by Leonard in a chapter of the fifth season:
Sheldon: You are my best friend Leonard. Why don't you ever take my side? Leonard: Because I never understand your side!
It's been shown that his friends have learned, at least to some degree, how to phrase things so he will understand. For instance, Sheldon didn't understand why he should buy Leonard a birthday present until the others told Penny to tell him it was a "non-optional social convention." Once it was couched in those terms, Sheldon fully understood the necessity and had no problem with the idea.
Sometimes discussed in Supernatural. Because of the nature of their work, Sam and Dean occasionally run into Pagan gods and monsters who see nothing wrong in killing and eating people in order to survive. Also, there are more than a few moments where it's abundantly clear that Castiel is operating from a very different moral framework to the Winchesters, which is arguably the biggest source of tension between himself and Dean throughout the series.
Damon might have this; he's a vampire, the natural predator of humanity, and thus can be severely out of step with what Elena and co. consider acceptable behavior. Perhaps most notably, when Elena asked him to remove Jeremy's memory of Vicki's death and when he... went overboard, so to speak, he genuinely did not see why she was upset.
It's also been stated outright several times that vampires can "turn off" their humanity, like a switch: freeing them from negative or connective emotions like fear, love, or guilt. This explains a lot. Stefan leaves his humanity "on" all the time, Isobel leaves hers completely off most of the time. Damon's humanity is "off" at the start of the series, but he's turned it "on" somewhere around the end of Season 1. It is stated by 500-year-old Rose, however, that the ability to shut off their emotions fades with age.
In Teen Wolf, Derek was born a werewolf, raised in a family of werewolves, and always does things the werewolf way. Unfortunately, this doesn't always align with anyone else's ideas of good and evil.
Person of Interest: Harold Finch, talking about The Machine and other artificial intelligences, observes that "our moral system will never be mirrored by theirs because of the very simple reason that they are not human."