In the first story arc, the Hollows are established to be human souls corrupted before they could be purified by the Shinigami. They eventually lose sight of their human lives. A Shinigami's job isn't just to kill them, but purify their souls and allow them to pass on properly. One of the reasons the Shinigami went to war with the Quincy is because their abilities out right oblierated a hollow, destroying the soul they used to be.
In the Hueco Mundo arc, multiple Espada explain that they see the Shinigami as the cruel ones because they slaughter Hollows mindlessly. Before Zommari dies, he rants to Byakuya about how Hollows are seen as evil and slaughtered simply because they need to eat humans to survive and says that Shinigami are evil, biased murderers. His defense falls flat considering that Hollows are, or were, normal human souls driven insane and twisted into monsters bent on devouring all around them. Their dimension is a boring void full of similar psychopaths who would destroy them in a nanosecond if given half a chance. Soul Society kinda sucks, but it's better than that. When defeated, the hollow becomes a plus and actually regains said sanity.
During the Turn Back the Pendulum arc, 4 of the Gotei 13's captains, 3 of its lieutenants, and the Kido Corps' lieutenant were immediately ordered to be exterminated because they were guinea pigs in hollowification experiments.
The anime's censorship makes one of these. Sajin Komamura, who had a caved in chest and severed arm, doesn't get his wounds censored in the anime like everyone else does (he even gets several more cuts across his body as Padding), when Hiyori was supposed to be cut in half, but is still whole in the anime (in fact the anime even replaced Tsukishima, a villain, getting his arm cut off with a gash). Reason? Because he isn't human but an anthro wolf. Either the writers only do this to those who don't look human, or just flat out hates Komamura.
Averted in Monster Rancher where Genki is equally compassionate to the less human looking monsters, even the ones who are trying to kill him.
The Mazinger series:
Mazinger Z: discussed. In the original manga, three Iron Masks broke in the house of The Hero Kouji Kabuto. During the scuffle, he learns they are corpses turned into cyborg by Big Bad Dr. Hell and they are just Empty Shells programmed to obey. when one of them tries to convince him to die and become like them, Kouji angrily yells such a thing not even would be human. Still, Kouji doubts about killing them, even if it is in self-defense, and when finally he gets forced to, he gets shell-shocked and later he wonders if he is not a murderer now.
Usually Kouji and his friends think nothing of obliterating a Mechanical Beast in horrific ways (ramming a fist through its chest or punching its head or limbs out, dismembering it, blowing it up to bits, melting it, turning it into a heap of corroded scrap metal...), usually treating them like unliving, unfeeling machines. However, if a Beast exhibits more traces of independant thought, they may be more reluctant to fight and even can feel sorry about destroy it (such like Spartan K5 or Jenova M9).
Minerva-X is a complicated case. She was a Humongous Mecha Dr. Kabuto designed. He programmed her to think independantly, acting on her own and even feeling emotions (including love). Everybody treated her like if she was alive and was a person, and mourned her death. And in Shin Mazinger Zero she has been traveling through time and dimensions, and we learn she is the original Minerva, so she MUST own an soul! Can it be said she is non-human, then? the implications are... unfortunate or mind-boggling.
Human-looking robots were treated like simple machines or human beings depending on the instance. The robots posed like Prof. Yumi or Kouji Kabuto were destroyed without a second thought. Robot Girls Erika or Lorelei were mourned when they died, and Shiro blamed Mazinger-Z for the latter's death and even temporarily hated him. However, the Gamia sisters were also Robot Girls and Kouji did not hesitate on destroying them (although he was very unsettled and even sickened after seeing their remains since they were REALLY human-looking). In Shin Mazinger Zero Shiro freaked out when he accidentally sliced one of them in half, thinking he had killed one girl, but his brother's friends told him she was only a robot to reassure him. The difference on treatment seems depending on how many human traits the robot exhibits rather what side it is on.
Great Mazinger: The Mykene are a civilization whose island was destroyed for an earthquake and were forced to seek shelter underground. To survive they grafted their brains into mechanical bodies. Therefore, the War Beasts are giant cyborgs once were humans, and they were more alive than any Dr. Hell's Mechanical Beast. However, Tetsuya and Jun never seem caring at all about destroying them. Then again, Tetsuya is a Blood Knight sees himself like a soldier fighting a war, and he accepts he can die at any time. So he treats the War Beasts how he expects being treated.
Duke did not particularly care about destroying Saucer Beasts... until a Vegan spy revealed to him that the Saucer Beasts he had been fighting are powered by the minds of his home planet's slain people (including his own little brother). Duke flipped out completely.
Before the outbreak of the war, Kouji was convinced Earth people could communicate with folks of other planets and become friends. After the Alien Invasion began, he did not seem feeling conflicted or remorseful about shooting faceless Mooks or Vegan ships. It was different if instead of an anonymous minion they had to confront an enemy they had got to meet and know about his/her personality or motivations, though. Then they could mourn him or her, regretting his/her death and wishing things could have been different.
Well, there's one Lost Strip where a Frenchman notices something odd about France, namely that he hasn't aged since the Crimean War. The 2011 version of the same strip tackles the issue more head-on, though France's answer is rather...cryptic.
More than a few fics explore the possibilities of this trope, though it usually doesn't go well for the Nations themselves. These themselves tend to result in them becoming either media freak shows or guinea pigs for testing.
And in the earlier 2007 April Fools event, Hungary suggests "exposing" France to the public as his punishment, though that may have just been her suggesting that he be paraded around in the nude..
Actively explored in Ghost in the Shell: Stand Alone Complex, which was inspired by the book and movie Blade Runner. The Tachikoma spend long periods of dialogue pondering and debating this subject. They are, in fact, the subject of the subject, and the main characters join in to varying degrees from time to time. Ultimately, the other members of the force start to treat them more like people than machines and value their lives more. However, the Tachikoma sacrifice themselves at the end of each season out of loyalty to their human friends. The first time, the Major notes that they were developing "humanity" and the second time Aramaki explicitly refers to them as "some of my men"
How many mechanical parts does it take before a human is no longer human? The Major acknowledges that except for the few brain cells she's left with, she no longer has any human components, but based on the idea that she has a "ghost", whether or not that can be confirmed in a laboratory, she's treated as a human.
In the manga version, this trope is subverted with the Tachikoma. During routine maintenance, one of them resolves to convince his fellow machines that they should have the same rights as humans, and in fact they are probably superior, and tries to start a revolt. The rest of the Tachikoma decide that humans aren't so bad and anyway if they overthrew them, there would be nobody to fetch them oil and give them maintenance so they treat the rebel as a lunatic. It's later shown that the so-called rebel was pre-programmed by Major Kusanagi to see what the reaction of the other Tachikoma would be, and whether or not they needed mind-wipe before a real rebellion occurred. The anime also has the Major worrying about the same sort of rebellion. (Her concern about the Tachikoma is painted as a bit hypocritical, since she herself is rapidly approaching the human/not-human line from the other side.)
Uncomfortably done in Dragon Half, depending on how far past the slapstick you're willing to look; various non-human creatures with speaking parts (as opposed to "intelligent"; they're usually really stupid) have been indiscriminately killed and sometimes eaten, but when an apparently human girl gets stabbed, everyone gasps in shock. It turns out she's actually a half-slime, so (a) that's all right, and (hopefully) more importantly (b) she isn't hurt anyway.
Lampshaded when during their first encounter Seras ascertains that Alucard is not a human before shooting him. Alucard derisively comments on that: "Why? Would you have shot me if I was?"
Seras and Alucard have no problems killing Vampires and Ghouls but Seras is disgusted after Alucard massacres Brazilian troops storming in their hotel room. Alucard rebuts her by saying that they were coming to kill them and that it doesn't matter what they are, human or not.
Nudist Beach considers Senketsu little more than a weapon whilst Ryuko considers him the same as a human being. The revelation of this send Ryuko into a rage and makes her refuse to wear him until getting a much-needed wakeup call after being brainwashed and forced to wear Junketsu by Ragyo.
To further accentuate her inhuman nature, Nui Harime is the only one to suffer permanent scarring and loss of limb, and that no one in-universe would actually feel, let alone show, her any pity.
The rule of thumb in Sailor Moon anime seems to be that if you're a Monster of the Week, you're dead meat. Even you do display some level of sentience. Since the monsters of the week are always artificial life forms and in many cases actually transformed humans or created from the souls of the humans the Senshi are trying to save, there's some justification for this. But it is amusing that the value of their lives is never discussed.
The manga is more ambiguous about this: most of the villains get killed by the Senshi because they're pure evil and remorseless, so this discussion becomes moot, but Minako knows from her experience that some of them are not (and in fact has an Heroic B.S.O.D. at the end of Codename: Sailor V (of which Sailor Moon is the More Popular Spin Off) after killing the last enemy of the series in spite of having realized beforehand he wasn't really evil)... And so, after forcing herself to go on and smile, is the one who kills the ones who she knows have a conscience.
One of Ga-Rei -Zero-'s prominent plot points is Kagura's inability to kill Class-D spirits (re-animated humans), to the point where she enters a Heroic B.S.O.D. because she was forced to kill her teacher to save her friends. She overcomes her naivety with pure Heroic Resolve (killing Yomi helped too).
This is also explored in Magical Girl Lyrical Nanoha A's. Mission Control has revealed that the enemy are in fact sentient programs, so "shouldn't be considered as people." Artificial HumanFate Testarossa comments that "they're just like me, then." Which results in a hasty response that really, she's just like other humans in that regard. Later as Nanoha confronts one of the programs who denies sentience, she retorts that if someone can talk to her and clearly have emotions (she had been crying for most of the fight), then it's obvious that they are people; just like humans.
It's suggested that the Wolkenritter were initially emotionless, but may have developed feelings as a result of Hayate's influence.
Magical Girl Lyrical Nanoha StrikerS also has this, tempered with a bit of Fridge Logic. A key part of Jail's plan is that he has clones of him implanted in the wombs of the Combat Cyborgs, who are actual perfect copies of him, ready to age to adulthood in months and resume his work if he is taken out. Many artificial humans in the series are given consideration, but it seems that all the fetus clones were summarily aborted.
In Samurai Deeper Kyo, countless humans are killed in several fights. In a possible example of executive meddling, the anime adaptation had all the evil characters turn into monsters at some point before they were dealt the fatal blow, possibly for the sake of preserving the good guys' "goodness".
In Trigun, the main character, Vash, refuses to kill any form of sentient life, including giant flesh-eating sand worms. Mindless sentry robots are another matter. The fact that he is himself a non-human sentient "person"/Ridiculously Human Robot may help. However, sentience doesn't seem to be the issue here so much as respecting all lifeforms (which the robots ...aren't?).
Vash placates the master computer and the robots stop, well, trying to kill things as a result. Considering the familiar, understanding tone he takes with the control room, he probably knew precisely what was going on.
In any case, the sentry bots were simply remote controlled extensions of the AI, which was unharmed (though annoyed) by their destruction, rather than independent intelligences.
In Robotech (and possibly the original Super Dimension Fortress Macross), it is only after the Zentraedi are discovered to be genetically compatible with Earth humans that the possibility of peaceful relations is even proposed.
In Macross Frontier, however, humanity eventually accept the Vajra Hive Mind as a sapient, friendly entity, despite the Vajra being Starfish Aliens who barely even understand the concept of individual intelligence without fold wave links.
The vagrant AIs in the .hack// series are treated as worthless and troublemaking pieces of data by the administrators, as is any human that sides with them. The main characters, naturally, see it differently. Nevertheless, they still left the game for good as a type of "growing up" metaphor, leaving the AIs to fend for themselves.
Kite returns in a manga set after the Dot Hack GU games, along with several fan favorites.
They mostly all die in .hack//GU, with the writers going after a different Aesop than the one in the first half of the franchise. The AIDA, unlike the aforementioned vagrant AIs, were attacking people and putting them into comas; including the protagonist's former love interest and the antagonist's little sister. That doesn't mean that their behavior's justified, but it makes it understandable. Also, the final attempt to kill the AIDA fails, deleting only their aggression, and there are no further attempts to destroy them after that. Also, there's a 'good' AIDA in the OVA, and Atoli offers the notion that Player and Aida can coexist peacefully.
This is a major theme in Plastic Memories. Given that Gifitias are gifted in having emotions as human beings, some do not take the business of handling and retrieving expired androids that well. This is lampshaded by Chizu during the first episode when she criticizes Tsukasa's company for treating her Giftia as a product rather than an actual family member. They are treated mostly identically to humans while alive though, and even have human rights.
A major theme in Bubblegum Crisis in all its incarnations (although the original OVA series is lighter on this content than you might expect, all told). The sexaroids Sylvie and Anri are more three dimensional and human than some human characters, and play a considerable role in Priss's acceptance of Boomers as being more than soulless machines (to the point that Sylvie and Priss's relationship, and its sexual/nonsexual nature, is a great source of online debate). That being said, the aforementioned boomers only appear in two episodes; the rest of the time, our ladies have no qualms about killing even seemingly sentient boomers.
In the remake, Bubblegum Crisis: Tokyo 2040, this was tied into the Myth Arc, when The Reveal showed that Sylia's brother Mackie, who throughout the series seems to be mysteriously the same age in both pictures of him from years earlier and flashbacks, is in fact a Boomer. Given the much-less-ambiguously monstrous nature of Boomers by that point, Nene's belief in his humanity (and her romantic interest in him) is what keeps him from simply giving in to Galatea's control. The Boomers of 2040 only go insane because they've been created as intelligent beings and then had their intelligence altered, enslaved and lobotomised by humans. (How true this is for the original OVA is unclear, though.)
Boomers in Bubblegum Crisis are partially biological, which might make you support them further. However, Adama from Bubblegum Crash! was a fully sentient fully non-biological android (which was significant for one reason or another), and once again, Priss was the one who got the Aesop.
In Gunnm, this is explored from every possible angle: human brains in robot bodies, human bodies with the brain replaced with a computer chip, even split personalities given bodies of their own.
Season 3 averts the trope by demonstrating that there is no difference between digital and organic life, since both Digimon and Humans (military, innocent bystanders, car drivers) die permanently (no Disney Death) in this series. This is especially interesting because the most mourned death was Leomon's and not one of the humans because the Tamers didn't witness it first hand. Early on, there is a debate/fight over whether or not to feed on wild Digimon's Data, strengthening the partner Digimon, which is solved very subtely They decide not to absorb the data, in hope that those that are too violent and have to be killed (those that were spared were killed by Yamaki with Juggernaut later on) are reborn elsewhere, which is later disproven when they arrive at the Chuchidramon village.
Strangely applied in the second season in regards to the good guys delivering killing blows to enemy Digimon. In season 1, the good guys were willing to kill enemy Digimon, as long as they weren't good Digimon infected with Black Gears. Yet in Season 2, the new generation of heroes is shocked and appalled by Ken and Stingmon's nonchalant killing of Thundermon during a fight, until it's discovered that it, along with other Digimon they encounter, are artificially made by control spires by a villain and are simply mindless drones (save for Black War Greymon, who was made from 100 and developed free will as a result). When the Daemon Corps attack the real world, the new kids are uncomfortable about killing them, while the kids from season 1 are okay with it. Largely because these Digimon were terrorists, whose acts of ruthlessness included threatening a bus full of children.
The sixth season plays it straight completely, since the human characters have zero compulsion to spare enemy Digimon, without knowing if they'll ever be reborn, despite calling digimon friendly companions in the opening.
Justified that they are in a war, and that they only defeat enemy Digimon. They generally do not attack friendly or neutral foes. Additionally, because the digimon that were killed were later reborn, the example falls into the exception opened by the previous series, the difference being that the protagonists didn't know beforehand.
Kurau, Christmas and other "Rynasapiens" in Kurau Phantom Memory get chased, abducted and generally regarded with great disrespect for the fact that they are half-alien hybrids with special powers. The matter gets confused since some Rynasapiens indeed have ulterior motives.
In the Cowboy Bebop episode "Jamming with Edward", the bounty-head is revealed to be an Artificial Intelligence that Ed had been interacting with. As AI are not considered organisms, they are not subject to having bounties placed on them, thus no bounty is awarded.
This is Sensui's dilemma as a teenager in YuYu Hakusho. Meeting Itsuki, a demon, after hating demons all of his life as a Spirit Detective, and finding out that they liked the same TV show- eventually becoming gaylovers was one of the catalysts the other being the Black Black Club for his fall from grace.
If your show includes a good guy who happens to be a suit of armor, homunculi, and human transmutation, you automatically invoke this trope.
Let's not forget that little girl turned into a chimera, that gets killed by Scar in what he considers to be a Mercy Kill. People do mourn her loss, but they had already started mourning her when she was turned, before Scar killed her. Everyone seems to be in agreement that killing her was a kindness.
In all fairness, Scar only killed her because he could tell that she was in great pain (no doubt due to her transformation). So to his way of thinking it was probably a Mercy Kill. Doesn't excuse what he did of course, but still.
Edward's inability to kill things seems to only apply to humans, things that resemble humans, and things that were once human. He has little issue killing animals and animalistic chimeras (which are made using animals). To be fair, the anime does show both him and Al killing their first animal, and it was done with huge reluctance. By the end of the 2003 anime, he has no qualms about killing the Homunculi, either - even though they're arguably more human than their manga counterparts. However, this also seems to be with some reluctance, given his freak-out over Greed dying, which he didn't intend since Homunculi normally take injuries as little more than a set-back. His later fights also had more on the line, since Alphonse was being targeted after being turned into a Philosopher's stone.
The titular girls in Gunslinger Girl are cyborgs, as a huge part of their body has been altered scientifically, yet they still act and seem like normal children for the most part. This causes even more of an issue as they're treated more like sub-humans and are made to be assassins.
Early on in Angel Sanctuary, Setsuna was urged to kill his best friend, Kira, on the basis that as the spirit of a bloodthirsty, evil sword, there was no point in allowing someone with just the facade of humanity to live. Setsuna refuses although considering Kira later turns out to have the soul of Lucifer, this might not have been in Setsuna's best interests. Kira himself struggles with his humanity or lack thereof throughout the series, generally insisting he never wanted to become human.
Astro Boy dabbles in this often. Atom/Astro, after all, was abandoned by his Mad Scientist father, Dr. Tenma, when he failed to serve as a complete replacement for his dead son. Astro is very into having robots treated respectfully and as individuals.
Human and robot relations in Astro Boy are driven up to eleven in Urasawa's retelling, Pluto. How human do humans see robots as? How human do robots consider robots to be? How do people feel about it getting harder and harder to tell man from machine? What do older robot models think about newer androids that outclass them both in body and in sentience? At what point do machines count as people? What about robot rights? How many more philosophical questions on artificial intelligence can we cram into the next chapter?
One-Punch Man: Saitama kills obviously-sentient non-human monsters (even ones whose inhumanity is physically slight, like a Cute Monster Girl) without the slightest hint of remorse; but he refuses to kill humans ever. This is particularly obvious in the Garou arc, where Saitama decides that Garou is human and won't allow the heroes to kill him. Part of this is that some monsters were never human in the first place. Those who were human typically went crazy due to a particular trauma or obsession and mutated; after the mutation, the monsters have lost all humanity and will slaughter and kill without rhyme or reason, so Saitama shows them no mercy. One reason he refuses to see Garou as a monster is that Garou won't kill other humans.
Saitama's standard, however, seems to be whether the monster is an immediate "lethal" danger toward people; he's let Garou and the weed monster live since they were only beating people, he's also let Black Sperm and Rover live (he even keeps them as pets) when they were in a weak form, and finally he's allowed monsters to surrender (Armored Gorilla was spared). He still shows a little more mercy towards full humans (he lets Sonic live, even though he never surrenders or stops being a danger).
Some of Kyon's biggest Pet the Dog moments in the Haruhi Suzumiya novels come from his treatment of Yuki Nagato, who is not only a near-robotic Artificial Human, but the big winner of the Superpower Lottery who verges at times on omnipotence. He treats her the same as he treats everyone else and refuses to use her abilities and obliging nature any more than is absolutely necessary, to the vocal surprise of the pragmatic Itsuki. His treatment of someone who is actuallyomnipotent as neither an object of worship nor something to be controlled is also an example.
The alien Arume in Blue Drop create synthetic children to function as bombs or as devices to clean up the remnants of their own biological weapons. All of them are female with bright blue eyes and white blood, just like the Arume themselves, and they grow up just like normal children. Quite a few earthlings definitely regard them as human and try to protect them from their fate and the persecution by earthlings. The synthetic Arume also share their creators' tendency to fall in love with earth girls, which makes things even more complicated and leads to a lot of drama in the manga.
Xam'd: Lost Memories features people turning into "humanforms", huge monsters that generally spew destruction. When the hero kills one in order to save another human, he gets called out on how he's being a bigot.
In Basilisk, the ninja are all technically human, but many of them are extremely freakish-looking humans. And there is a clear tendency for the more grotesque ninja (Jimushi Juubei, Kazamachi Shougen, Azuki Rousai...) to die first.
In the adorably squickyAlien Nine series, elementary school girls bond with deadly alien symbiotes that look like winged fish helmets to combat alien invasions, or alternatively extinguish spy rings preceding invasions. The symbiotes are experienced at this sort of thing... the girls... less so.
Averted most significantly by Keiichi in Ah! My Goddess. He's willing to reason with others, regardless of what they are. He even aided the demon angel, Blue Lance.
The titular character's "good" qualities are measured by his unwillingness to kill humans, even horrifyingly evil ones. However, he kills youkai without a second thought. This is true of all the characters, but it's a little disturbing with the youkai and half-youkai: the "good ones" are the ones who value human life, but seem to place no value on the lives of their own kind. It seems like even humans who are murderers and rapists are worth more than demons who are little more than irritating pests.
Kagome's bizarre insistence that Inuyasha "may be half-youkai, but is half-human, too," so he can be a good guy is strange given that she's traveling with a full-youkai, Shippo, who is the most innocent member of the cast.
There was one youkai who was ordered to steal Tessaiga from Inuyasha. After he was caught, Kagome said, "If you do it again, we'll slay you." This is in direct contrast to when Sango stole the Tessaiga and nearly got the group killed, where she was easily forgiven.
There is a notable exception to the half-youkai rule with Jinenji, a large, ugly (but benevolent) half-youkai that was being discriminated against by the village he lived in, only for Kagome and (especially) Inuyasha to take his side and get the villagers not to see him as an enemy. This trope is actively explored and played with throughout the episode.
In the Band of Seven arc, Inuyasha spares Jakotsu after he defeats him because the latter is a human being. At the time this happens, however, Jakotsu is an undead, not to mention a sadistic murderer who has already killed many humans.
In another arc, Inuyasha destroys a whole pack of bat-demons because they're mistreating the young half-demon girl Shiori, yet he seems to do nothing against the humans who have also mistreated Shiori.
To be fair, it must be mentioned that the protagonists have frequently spared antagonistic youkai if they were not really evil, or at least have not killed humans. With Koga and Sesshomaru, they have even become friends, even though they were evil youkai at the beginning.
Hanyuu Furude of Higurashi: When They Cry is a goddess. However she was originally seen as a monster to many villagers due to her horns, though it turns out she's a normal human with a physical condition. She is ritually sacrificed by her reluctant preteen daughter, Ouka, as Hanyuu thought her sacrfice would cause all the villagers sins would be atoned. They didn't and Hanyuu is regretful of it centuries later. Good 'ol Hanyuu.]]
In Video Girl Ai, the Video Girls are Robot Girls specifically created to help humans who are good-hearted and need emotional/moral support. However, they're supposed to follow only the orders of their creator and/or the needs of the client. Then, one of the Video Girls has her tape played in a broken VCR... and she starts to develop human-like feelings, like falling in love with the Unlucky Everydude she's supposed to aid. As punishment and/or preventive measure, she should have her tape returned and then be "rebooted", but is this the right option? Or should said Video Girl be released and allowed to pursue her own goals? And let's not even think of what would happen when a Video Girl is assigned to an actual pervert...
Elfen Lied seems to decide that yes, Diclonii are people too. And then they're all exterminated to preserve humanity.
In both Appleseed movies all cyborgs besides protagonist Briareos are expendable, and mostly evil. The Final Boss at the end of Ex Machina is even more blatant version of the trope - she's been resurrected from the dead with cybertechnology, and as result has become something of a Borg Queen. However, the protagonists manage to briefly medicate her with micromachines and bring her back to her senses, at which point she begs to be allowed to die as a human. When two of the three protagonists present are a cyborg and a Bioroid, both very clearly fully functional people.
The Witchblade anime played a with this, in different forms. That is, would it be okay to use dead bodies as reanimated soldiers with electronic 'brains?' And if that soldier's conversion is a successful model, what about cloning him, but as the state he is now? Masane is at first horrified when she discovers the X-cons are modified humans, and iWeapons are made of human corpses. Takayama just considers this to be more expendable than living human soldiers. And NSWF producing the cloneblades and wielders for them are more squicky. Then there's one Tyke Bomb obsessed with attempts to understand who and what she is. And several quite "real", but batshit insane humans.
In Darker Than Black many people aware of them think Contractors and Dolls are "no longer human". Dolls may be sold and treated like furniture or devices, Contractors are perceived as a sort of killer robots. Not that there weren't any reasons at all for such an attitude, but...
In Pretty Cure the girls complain about having to kill the first villain and are told by their Non Human Sidekicks that they're just making him "return to the darkness". Later they find that Kiriya does a Heel–Face Turn... incidentally proving that the enemies aren't Always Chaotic Evil after all and killing them should count as killing people, which is never even mentioned. This line becomes heavily blurred as the seasons go on, to the point where the teams' powers are reclassified as purifying than outright "destroying". Also, it's quite rare to see a show's main villain be outright killed and if they are, it's a Redemption Equals Death sort of death.
In Waq Waq, Shio, the son of a "Guardian" tasked with defending villages from machines, initially struggles with this after meeting the friendly Pura, but comes to the conclusion that humans and machines can be friends.
While the Bugrom were in the process of conquering the humans in El-Hazard: The Magnificent World, you'll notice that no one seems to care the OVA ends with nearly their entire race being sent to another universe because they're 'icky bugs'. The fact they display signs of intelligence and personality around the one human to speak their language is ignored.
In Mahou Sensei Negima!, Chachamaru wonders if she has a soul and can therefore make a pactio with Negi. But as far as the story goes, she definitely qualifies as 'human' as do the local vampire, the half demons etc. But the other robots like Tanaka are definitely just machines, despite speaking on his first appearance. Presumably because they all have the same form, and it's not a cute one like Chachamaru's. And their not as much Magitek as she is.
The official position on the souls of artificial beings is if they're capable of desiring a soul, they have one. Chachamaru's soul was confirmed when her pactio with Negi worked—though considering it only did so after Negi turned his kissing Up to Eleven, he may have cheated on this one.
Magic is just racist. Or Model Number-ist. Or Type-ist. Or whatever it would be that applies to robots.
Also referenced with regards to Negi himself once his Dangerous Forbidden Technique starts turning him into a demon. Its explicitly stated that he'll be a higher level of being, but he'll also become "a beast", no longer human.
However, this doesn't quite count in reference to this trope. Even though Negi would be no longer considered 'human' he would still probably be considered a person, as Negi definitely considers Evangeline, a vampire, to be a person, and the end result of turning into a beast was commented to be similar. The better example would be Kurt Goedel's plan to sacrifice all 'nonhumans' on the Magic World in order to save the Magical Humans.
Subverted in A Certain Magical Index for clones. About ten thousand MISAKA clones have died already, one dies at the start of episode ten and another at the end. However, after that Touma gets pissed about how they're viewed as being so expendable for such a stupid goal and the next one is saved and the project halted. The original for the clones was already on her way to die trying to stop, and even the guy killing them always spoke to them first to make sure they weren't 'real' people who had goals etc and feared death. They hadn't lived long enough to really form proper values like that, hence ten thousand casualties.
Kazakiri Hyouka Fuse=KAZAKIRI is an interesting example of this as she is an individual consciousness and yet is also a sentience of the AIM field created from all the Epsers of Academy City. In particular, she decries herself as a monster (twice in the anime, at least) and it's Touma and Index who say otherwise. That doesn't stop Aleister from treating her like a tool as suits his needs.
Tree Diagram is considered the pinnacle of Science-side artificial intelligence. It is destroyed at the start of the main series and, despite a crushed attempt to rebuild it for the purposes of continuing a cruel experiment, largely goes unmourned.
If you can look past the rampant fanservice, cuteness and comedic moments, this is a major element explored in Chobits.
Vampire Princess Miyu. OHSOMUCH. The Shinma, especially humans made into ones, can be endearing, if villainous. If anything, poor little Hiyoku...goes through hell, turns into a Shinma and expects life to be better, only to get fried. Also related to this is the pair of good rogue Shinma who end up frozen by the Queen Bitch Reiha in the Light of the Sea arc, and some others.
In the Yu-Gi-Oh! English anime, the deaths of human characters (as well as many threats of death of human characters, like Marik's Rare Hunter duels) are censored with banishment to the Shadow Realm (for instance, instead of Marik stabbing his father as he did in the Japanese version, he banishes him to the Shadow Realm). They do not seem to have a problem killing off monster characters, like the Great Leviathan and Zorc, or evil spirits like Yami Marik (though Yami does say he will "vanish into the Shadow Realm", but he seems to explode nonetheless) and Yami Bakura. A few exceptions to this have been made; Mahad is destroyed, though he becomes the Dark Magician (a Duel Monster) first. Cecelia Pegasus is said to have been killed by an illness, and of the seven who perish in the virtual world when it is destroyed (Gozaburo, Noah, and the Big Five) only Noah's death is censored (because he is the one who turns good), by the characters speculating that he saved his mind on a backup drive. However, in this case the Big Five are all imprisoned in unseen corners of the virtual world as it is destroyed (and have barely been mentioned since their defeat), and therefore their deaths are offscreen, while Gozaburo transformed into a fire monster at the end and survived for a few seconds, as a beast of fire in the real world, where he attempted to eat the blimp and everyone in it.
Mostly averted in Slayers. The protagonist humorously blow up non-human and human mooks with equal enthusiasm, although there are more non-human mooks that attack them. If any bloody slaughter is shown, it's always of non-human races, but the story and the protagonists don't treat it as if it isn't terrible. Perhaps the series uses this trope because dead humans will get them M-ratings, but they avoid most of the Moral Dissonance.
This is pondered upon by Uragon from The Tower of Druaga, which surprises some viewers since he was The Neidermeyer up until that point. This came up after he saw that he was the only one who wasn't visited by anyone when the various groups ended up at the House of the Dead (no relation), and found one of Pazuz's magic knights when he sat down on a bench.
Contemplated in Rumiko Takahashi's Mermaid Saga. The monstrous, violent "Lost Souls" —humanoid, scaly beasts with frog-like appearances and enormous strength— are the remains of an unlucky human who ate mermaid flesh and neither died instantly nor became immortal. For the most part, they're treated as Giant Mooks driven by instinct and prone to violence, so the protagonists destroy them in self-defense with nary a thought. But then Mana is saved by one who retains enough intelligence to dress in robes and hide his horrifying demeanor from others, even living as a hermit in the woods for his own safety as well as other people's (although he also has the strength to dig Mana out of a landslide or tear a deer's head off in order to feed.) Mana comes to understand him and realize that, even as a Lost Soul, he's kind and gentle and wants to keep her safe... but neither Yuuta nor the villagers know this, and the Lost Soul is killed as all the others.
It first occurs in inverted form; the Arlong Pirates believe fishmen are a superior race and humans exist to serve them.
It occurs again in Sabaody Archipelago. Humans view fishmen and merfolk as lesser beings and enslave them. In fact anyone that isn't a normal human is viewed as a lesser being, including giants and mermaids. Regular humans can also be enslaved and are then treated in a similar fashion.
The Celestial Dragons think that everyone is inferior. They are allowed to do anything they want to almost anyone. One Celestial Dragon rides on a human slave, kicks a dying man out of a stretcher, forces an engaged woman to marry him, and shoots her protesting fiancé. All of this is done within minutes of his first appearance.
Tony Tony Chopper plays with this trope on the boundaries of human and animal, being the only one of the crew who is not human and never was, but merely adapted his humanity from a devil fruit, though surprisingly the series rarely addresses it outside of his own back-story flashback.
It is kind of addressed by the fact that the government seem to think of him as the strawhats pet and not as a crewmember. Thus his lack of a real bounty.
Bartholomew Kuma lives with this trope in a manner similar to Major Kusanagi, where he gradually loses his humanity as more and more of him is changed to cyborg, though in Kuma's case there was a distinct line drawn by one last procedure to remove his independent humanity entirely.
The zombies of Thriller Bark were usually treated as Zombies according to the norms described in this trope, except for Cindry, who does somehow gain a bit of her old humanity back, before being killed.
This is a bit odd because they took on the personality of the person who's shadow they used, rather than their corpse. The people who own the shadows are all still alive, and the shadows return when the zombie is "killed". Without their shadows, they can't go out into the sun, so it isn't much an option to keep both.
Remember the Seakings, giant creatures living in the oceans and casually cut in half either for feeding the prisoners of Impel Down or because they simply were in the way of someone? Flash forward to the finale of the Fishmen Island Arc, where the exact same seakings that the crew encountered during their attempt to cross the Calm Belt are revealed to be highly intelligent, able to talk to you through your mind and knowledgeable of some of the most ancient prophecies. How this will affect any of the characters and their dealings with them remains to be seen. However, their latest antics suggest that they continue to have no qualms whatsoever with using them as a source for food.
Of course, assuming all of them are intelligent, they don't seem to have a problem smashing apart whole ships or devouring humans whole, so it goes both ways.
More generally, giant animals (not just Sea Kings) in One Piece are frequently sliced in half by protagonists for being territorial/hungry/in the way. This wouldn't be so jarring were it not for the fact that even the most murderous human and humanoid villains in the series—some of whom have killed friends/mentors of the heroes—tend to wind up beaten and humiliated by the protagonists but very much alive. The fact that the heroes seldom use this same non-lethal force to deal with non-humanoid enemies suggests that they don't value animal lives much.
In Zettai Karen Children, the conflict between humans and espers generally falls under another trope, but in one episode this is tackled head on, when Minamoto argues for the destruction of Momotaro on the grounds that he's an animal, not a human, and a dangerous one. The Children veto this rather forcefully, and Sakaki notes that "they see him as one of them." Later, Kyosuke (an esper) challenges Minamoto to shoot him down in front of Kaoru and show her how humans treat "dangerous animals." He doesn't take the shot.
This is a major theme in Time of Eve. A particularly jarring example is when Akiko, the resident Genki Girl, is seen in the protoganist's school with her ring. A passing student simply tosses a bag at her.
In Naruto, humans have imprisoned the Tailed Beasts and been using them as living weapons for centuries despite the fact that they are sentient. This turns out to be the reason the Tailed Beasts hate humanity. The same happens to the humans who serve as the Tailed Beasts' vessels, treated as weapons and monsters instead of people.
Starting to come into play in Pandora Hearts after The Reveal that Oz Vessalius is not human but rather the chain B-Rabbit. Jack Vessalius, whose body Oz's soul is inhabiting, delights in tormenting him as he tormented B-Rabbit in the past, telling him that because he isn't human, his suffering amounts to nothing. He succeeds in completely breaking Oz emotionally when he tells him, "The people you love and the people you wish to protect... All that you've achieved... It's all fake. You've never really had anything to call your own anyway." Fortunately, Alice, who herself is not entirely human, is horrified and enraged at Jack's treatment of her treasured sentient rabbit doll Oz to the point where she is literally Driven to Suicide so as to keep Jack from further harming him.
Furthermore, Oswald-Glen ordering Gil to shoot Oz without any regard to the strong bond the two share seems to imply that he does not consider Oz an actual human being and that he sees him only as the B-Rabbit as well as a host body for Jack.
This topic is a constant point of contention in the world of Gangsta.
In Martian Successor Nadesico, the Earth is being invaded by the alien "Jovian Lizards" - as they are unseen reptilian monsters, it's nice to kill them and destroy their ships. They're not: The Earth government hides the fact that Jovians are lost human colonists, because if that be public, the Earth soldiers would be reluctant to fight the Jovians. In fact, once the crew of Nadesico discovers this truth, many crewpeople refuse to fight the Jovians.
Quite a lot of this trope going on in The Animatrix, but perhaps the most jarring example is a short scene in The Second Renaissance Part I. As it opens, you see a group of men pushing around a young, defenseless girl—a scene of physical abuse made more chilling by the fact that it's uncomfortably common in Real Life. Then one of the men hits her on the head with a sledgehammer, revealing robotic circuitry under her skin. She tries escaping, as another man rips off her dress for additional implied rape imagery. Then she is shotgunned to death, with her last cry being "No! I'm real!" You see, she wasn't even a woman, she was just a robot, so it was alright for big manly men to abuse and kill her.
One of the major themes of Sekirei, as the titular beings are essentially Human AlienMons raised by a Mega Corp. to take part in a cruel game of There Can Be Only One. They are dehumanized in a variety of ways, from having a number and being given a personal name only as an extra identifier, being subject to a monthly Measuring Day to gather data on them, and even sometimes treated like prizes to be awarded to the winner because it'll spice up the Game. Each Sekirei has a destined master (an Ashikabi) they're meant to be with, an explicitly romantic bond that strengthens them through The Power of Love......however, they can be forcefully bonded to be different master, an action fully encouraged by the Game Master. Not all Ashikabi are kind to their Sekirei, with some treating them as disposable or outright abusing them, as many are Submissive Badasses that will tolerate mistreatment rather than suffer their bond being broken. These types see nothing wrong with their actions, since the Sekirei aren't human and belong to them, right? One of the primary goals of the protagonists is to set the Sekirei free, since they're people and not things.
In Durarara!!, a few hoodlums are up against a "shadow". While they've killed before, the narration explicitly notes that they don't feel there's anything wrong with trying to kill it. Said "shadow" is Celty, Headless Horseman, Cute Monster Girl, and the main character. Oh, and a badass, so they really didn't have a chance.
In Neon Genesis Evangelion, the heroes tend to have little issue with killing Angels, most of whom display little sentience. It is only when Shinji kills Kaworu, a teenage boy and the final Angel, that he shows any real remorse or regret.
Puella Magi Madoka Magica: INVERTED. Kyubey, an alien who looks something like a cat or a weasel, cares nothing for the death of all the magical girls he contracts. Part of this is because he's from a species of sociopaths who view emotion as mental illness, but he still compares his relationship to humans as similar to the relationship between humans and livestock; both are raised for slaughter by the dominant party but he is more respectful. It gets taken a step even further later on however with the existence of the wraith system. While producing less energy than the witch system, hunting wraiths instead still provides energy to stave off entropy. However despite this the Incubators pursue research into the original witch system again even though it both causes an extreme amount of suffering for the witch and is highly dangerous to everyone else on the planet. The implication being while they may originally have been using necessary evils to preserve the universe, now that a second option is available they really just flat out don't care about the damage they cause to humans.
This is a major part of the Gundam mythos - Newtypes, Coordinators, X-Rounders, humans with amazing powers, but seen as little more than weapons for their war machines. Even worse, you got humans who are modified to combat these people, too.
And then there's the actual aliens in Gundam, the ELS of Gundam 00 Awakening Of The Trailblazer. In one scene, a human politician is seen saying "Hold on, we're talking about hunks of metal here! They aren't even alive!" Comes to a head in some of the side stories, which talk about a revolt against Innovators and ELS (and especially ELS-Innovator hybrids) by humans fixated on maintaining "pure humanity".
In Tokyo Ghoul, ghouls - with the exception of their kakugan and kagune (which only manifest when they're near-starving or in a fight) - are visually indistinguishable from humans, but eating anything other than human flesh makes them violently ill and impacts their health. While some of them are prolific serial killers, peaceful ghouls (who stick to collecting corpses from suicide hotspots and the like) are also treated as fair game by the Doves, and citizens are encouraged to turn any suspected ghouls into the CCG, where they may be tortured for information (at least one of the worst villains was created this way), experimented on, and have their organs extracted for use in anti-Ghoul weaponry. Early on, the protagonists ask a CCG employee if she feels conflicted over hunting down a child ghoul, only to be cheerfully told there's nothing wrong with it because ghouls aren't human. The result is a long-running and vicious Cycle of Revenge stuffed to the brim with Van Helsing Hate Crimes.
Completely averted in Monster Rancher, where despite the main character Genki being a human boy, most of his companions (except Holly) are very much not humanoid. This includes a blue horned wolf, a giant rabbit, a rock monster, a massive yellow eyeball, and even an armored mochi monster. This also extends to many of his non-human enemies, whom Genki will try to save (including a robot who developed Fantastic Racism towards humans for exactly what this trope implies). Some of the Big Bad's most monstrous looking minions even performed Heel Face Turns, among them a bug-looking wolf, and a serpentine lizard man, while some more attractive and humanoid antagonists remaining unrepentent. Even the Big Bad Moo, an evil overlord whose true form is a massive dragon, was once Holly's father whose body became possessed by the villain's soul.
Saiyuki. A great deal of the human/youkai conflict is blamed on the Minus Wave that led to numerous youkai going berserk, but it's clear that this is not the cause of all the Fantastic Racism. There's Hazel, who believes that the only way to solve the situation is to exterminate all youkai (including those that remained sane due to being young children or constantly wearing limiters), and who finds it fair to use souls of the fallen youkai to resurrect humans; there are "reborn" youkai who had their instincts unlocked by the Minus Wave and view humans as food. Sanzo, however, averts this, because he doesn't truly care if somebody is a human or a youkai; despite his well-deserved reputation as a youkai slayer (and countless groups of random youkai getting killed by him all the way through the manga, with his followers openly competing in the number of kills!), he will kill pretty much anything of any species — but only if it dares to stand in his way or sufficiently piss him off. His companions are also unique in that they're technically neither human nor youkainote Goku is a godlike being born from the Earth itself, Hakkai is a human turned youkai, and Gojyo is a half-human/half-youkai and find it difficult to properly fit into any group that's not "Sanzo's party".
In Cross Ange, most of the characters have no problem at all slaughtering the DRAGONs, but will balk if asked to kill a human being. When it comes to light that the DRAGONs are actually human (heavily genetically modified humans, anyway), the main cast doesn't take it well. Ange is shown vomiting from the sheer horror of knowing she's ended human lives. Mana based society is another story: Normas, which make up the bulk of the cast, aren't even considered human to begin with.
Notably averted in Daily Life with Monster Girl, despite expectation: the "monsters" are really just "Human Subspecies". The problem they face is common human prejudice akin to different minorities rather than being being alien species, leading to a different trope entirely. This is mainly because 1) they've always existed, rather than as a fantasy introduction; the human government has just kept them hidden and 2) they are indeed "human subspecies" and for the most part they act like humans with physical quirks; in fact, humans and some extra-species have always reproduced together and the zombie extra-species is, in fact, composed of actual former humans anyway.
Space Battleship Yamato 2199 explores this in the episode "A Clockwork Prisoner": the crew capture a Garmillan android soldier, which Analyzer, a robot serving on the Yamato, builds a rapport with and dubs "Alter". When covertly exploring the Yamato's mainframe, Alter encounters a "goddess", which it pursues, breaking free from confinement and putting the ship on edge. While security searches for Alter, Executive Officer Sanada and Security Chief Itou end up arguing over whether Alter could be considered a living being, with Sanada positing that Alter's artificial intelligence is not unlike a human brain. When Itou sarcastically asks Sanada if he thinks Alter has a heart, Sanada throws the question back at him, wondering if Itou had a heart, himself.
Discussed in Kimi to Boku when the boys converse about how festival games involving catching fish with thin nets is toying with their lives. They say the man who owns the booth doesn't value the goldfishes lives enough. They end up getting him so mad that he gives them better nets, which lets them catch multiple fish.
In Claymore there are female warriors who are hybrids of humans and youma. And youma are "demons" that eat human entrails. The humans despise and fear them, or hate them even, and refer to them disparagingly as "silver-eyed witches". For almost all humans these female warriors are no more than youma. But they themselves see themselves as humans. It is also an important thing for them that they do not become a Awakened Being, because then they lose their human mind and would become monsters, also mentally. And indeed the anime shows many humans as evil, but that most warriors are really good.