In Hellsing, it turns out that the Major is a full-conversion cyborg. Subverted in that he still claims humanity because he has a human brain, and that they would be perfectly willing to kill him if were human anyway.
Inverted in Vandread. The idea of harvesting body parts from humans is so repulsive to the main characters that they assume their foes cannot be human. They are human, and from Earth to boot.
In Naruto, this is the opinion many people have in regards to jinchuuriki, and people doing so is a serious Berserk Button for the titular Naruto.
When Naruto powers his way into the 4th Ninja War, he's told that the enemy army consists of plant-monsters and undead ninja. His response is basically, "Good! Now I don't have to hold back!" In this case, it's more a matter of "The enemy won't die so I can beat on them with impunity."
One of the old Johnny Turbo comics ends with this revelation against the strawman "Feka" corporation. Actually somewhat necessary to inflame the reader and justify Johnny Turbo's excessive violence, since the only crime Feka commits during the comics is doling out inaccurate information about video game systems. And making little kids cry by doing so.
Amusingly, the Robotic Reveal only comes about because of said excessive violence, making it utterly ineffective as a justification.
Shortly after Doom 2099 has taken over the US, he learns that Avatarr, CEO of Alchemax and one of the main Big Bads of the 2099 universe, is in fact an alien trying to rule the world via Mega Corps. Of course, Doom only learned this after he shot the guy's eye out.
The film 300 uses this in one of the scenes where the Spartans are fighting the Immortals. A Spartan rips off an Immortal's mask to reveal that... They're Not Even Human! There's no suggestion anywhere else in either the plot or actual history that the Immortals were anything but, you know, just humans, albeit ones working for the supposedly evil Persian Empire. Or it's blatant propaganda by an Unreliable Narrator.
Inversion: The 13th Warrior. The fact that the I'm a Humanitarian monstrous attackers are human prompts the hero (and by extension, the audience) to be more horrified than when we thought they were monsters. After all, people have a choice.
Stargate. While Ra was a long-lived alien in a human body, his Mooks were humans, and it never stops anyone, in the movie or shows. (Not that it isn't justified in these cases: they shoot back when shot at. It's just that Ra didn't become more killable by proving non-human: Thou Shalt Not Kill was never in effect.)
Who Framed Roger Rabbit: "Holy smoke, he's a toon!" Normal toons aren't evil, but the reveal that the villain is one as well makes him both inhuman and much scarier in hindsight. He has been gleefully Dipping his own kind, and actually invented the chemical mixture that rendered his essentially-indestructible fellows vulnerable. Meaning this makes him even more of a monster than had he been human.
Also crosses with One-Winged Angel because up until the steamroller an ending in which the police show up and arrest him was reasonable. It's already clear he doesn't have the psychological vulnerabilities which allow a toon to be restrained, and the revelation (complete with turning his body parts into power tools) pretty much puts him beyond imprisonment or subdual entirely.
The sadly bungled movie Ultraviolet: in the final fight, Daxus turns out to be a "vampire" like Violet herself. Except that in the book, he just had night-vision goggles.
The Lost in Space movie - actually, it's a case of the villain becoming a monster, but it has the same basic results, very baldly stated.
The Lawnmower Man brings up the trope by name near the end (though not as a surprise, just underlining how far he's gone).
At the end of The President's Analyst the good guys storm The Phone Company headquarters to rescue Dr. Schaefer. When the backup power comes on, they realize the TPC president is sitting nearby as he starts to politely admonish them for breaking in. After a few uncertain moments they realize, to their amusement, that he's an automaton.
Don: He's a recording!
Kropotkin: It's like a visit with Abe Lincoln at Disneyland!
In the climax of The Brothers War, it's revealed that Urza's brother Mishra has been cyborgified, showing Urza that there's no hope left for peace or even victory. Foreshadowed earlier, plus there's the fact that the Big Bad himself is an even-more-advanced cyborg. Cue most awesome scene of mass destruction ever.
Similarly, in the prequel novel The Thran, Yawgmoth's troops in the final battles are bizarre Magitek cyborgs, including some former colleagues of the main characters.
Later, in Planeswalker, Urza is trying to eliminate Sleepers, Phyrexian artificial humans secretly infiltrating the population of his home world of Dominaria. Heck, Planeswalker proved that Yawgmoth was most definitely asleep at the helm, er, hub, of Phyrexia when the first batch of Newts were made. The kicker — somehow, despite having once been fully physical and human himself, a few millenia ago, Gix managed to forget that humans have different genders and reproductive, as well as waste, systems. The entire first batch of Newts (the Sleepers) looked human, but mostly teenaged boyish, with no genitals whatsoever — and glistening oil for blood. Way to go there, Gix, you schlep. This was improved on in later batches, of course, but this mistake proved costly for Gix...
It is emphasized in Harry Potter that Voldemort has made himself less than human in some ways. Namely, by splitting his soul.
Although no one suggests that it's okay to kill him because of that, it seems it's okay for the heroes to try to kill him because he's a murdering psychopath specifically trying to kill Harry. (Though being a murdering psychopath is a prerequisite for splitting your soul in the Potterverse, so there's some overlap.) And : he eventually gets killed in self defense. Although destroying the horcruxes is, in a way, partially killing him, and that is not done in strict self-defense.
And, in the case of Harry and his friends, it's also self defense, as he's trying to kill Harry.
Inverted in an early H.P. Lovecraft story, in which a man lost in a pitch-black cave hears something large and mysterious shuffling nearby and kills it with a rock. When his guide returns with a lantern to find him, they realize that the dying creature is a human being who'd been wandering in the cave for years, degenerating into an ape-like state.
In The Silver Chair, the Green Witch turns into a giant snake, at which point Rilian believes it's all right to kill her. Though this isn't just because she's no longer human, but because she's no longer a human woman; Rilian Wouldn't Hit a Girl.
Live Action Television
Happens with individuals often enough on Buffy the Vampire Slayer that people eventually stop being surprised by it. It plays an important part in the episode "Ted", specifically.
The Torchwood episode "Countrycide" features a Cannibal Clan living in a small town as villains, with no aliens or alien tech present in the story. The audience surrogate, Police Constable Gwen Cooper, was much better at handling the revelation of the existence of aliens than that humans could be so terrible.
The Supernatural episode "The Benders," when it turns out that a family of hillbillies has been abducting and killing people. Dean said it best:
Dean: Demons I get. People are just crazy.
The homicidal inbreds from The X-Files episode "Home" weren't supernatural or robots or anything else non-fictional; they just had a whole lot of genetic defects that exist in real life.
Smallville tries to resolve Thou Shalt Not Kill with Clark destroying Brainiac by invoking this trope. It's just a machine after all, despite all the characterization and its struggle to survive, right? Nicely accounts for Superman's irrational commitment to the idea that machines are never people, though.
Averted with Doomsday. Everybody else is trying to convince Clark that his true form is a mindless killing machine, but Clark refuses to give up on the fact that there's a perfectly ordinary human/kryptonian/something that would be killed in the process.
Played straight AND inverted in an episode of the most recent Twilight Zone series. A team of commandos is hunting a monster in the forest; said monster is very cunning and manages to kill all but one of the commandos, who is captured and taken to its lair. Turns out the monster is really a disheveled human. The reason why he's hunting people? The commandos, the people in the city, everyone is really an android; they overthrew humans long ago and copied their society.
It appears rather often on Charmed, and in one case the whole episode ("Mr. and Mrs. Witch") plays itself out without the Charmed Sisters ever becoming aware of it. The Monster of the Week is in fact a demon, but he appears to be a human Corrupt Corporate Executive. The demon is quite aware that the Charmed Ones won't kill him as long as they think he's human, and in fact the Charmed Ones never do find out. The demon is still vanquished by his superiors for failing to accomplish their evil plan; and in fact, the Charmed Sisters read about this evil executive's "suicide" in the newspaper, without ever being the wiser that this was a demon who they could have dealt with by vanquishing him.
Said word-for-word by Detective Mike Cellucci in Blood Ties to Henry Fitzroy after figuring out what he is. He says it with such disdain that Henry performs a Neck Lift on him in anger.
In BIONICLE, Kiina and Ackar are reluctant to kill the seemingly-humanoid Rahkshi. However, after one attacks Kiina, Ackar decapitates it and its Kraata falls out, revealing that "They're just slugs in armour". Our heroes have no problem hacking them to pieces after that.
Snake's Revenge, the non-canonical NES sequel to the original Metal Gear, has Big Boss revealing at the end that he was forced to undergo a transformation into a cyborg in order to survive the injuries he sustained in the first game.
Metal Gear 2 for the MSX2, the canonical sequel, parodies this by having a character gossiping that Big Boss may had become a cyborg and then subverts it by having Big Boss killed with a mere makeshift flamethrower.
Censorship laws in certain countries, most notably Germany, turn Video Games which originally had human opponents into this trope: the enemies look human, but it quickly becomes clear that they're not. And by "clear", we mean they palette-swapped all of the blood from red to green. So perhaps they're really Vulcans?
Fallout 3. President John Henry Eden, crapshooting AI at your service. Not even a humanoid robot, just a monolithic computer with delusions of grandeur.
Not that Fallout as a series has anything against good characters killing humans left, right and centre...
But only as long as it's in self defense (at least most of the time). Still, considering that out in the open wastes, essentially everything is trying to kill you, and preemptive strikes are a valid tactic...
Subverted in Mega Man 2. In the final battle, Dr. Wily reveals himself to be an alien of some sort, but after defeating him you find that the alien was really just a hologram that Wily controlled from a machine in the corner of the room.
This was originally planned to happen to Breen in Half-Life 2, revealing that he had become an immortal cyborg in the final battle. This was ultimately scrapped, although some fans speculate that he may have been turned into an Advisor.
Alex Mercer: I'm not human. The revelation...it freed me. It killed me. I'm not human. *uneasy chuckle* Alex is just the role I play. Part of me was relieved...and part of me died. Just another disguise, right? So ingrained...so real...even I believe it.
Of course, this is somewhat subverted by the real Alex Mercer being an even worse human being than the Blacklight virus.
Sam & Max Season 1: The Big Bad Hugh Bliss turns out to be a colony of sentient bacteria.
In Wolfenstein, the evil General Zetta appears to have the ability to shoot magical balls of energy out of his hands and blocks bullets with his mind. Turn on your spectral vision, though, and you see he's really a giant slug monster; apparently being exposed to the Black Sun dimension turned him into a monster.
Almost all of the human(oid) villains in Breath Of Fire 2 reveal themselves to be some kinda of monster before they're fought. For example a Crooked arena organizer turns into a two headed humanoid wolf when challenged.
Quoted by Shepard in Mass Effect to Sovereign. (Full quote: "You're not even alive. Not really. You're Just a Machine and machines can be broken!"). Sovereign, being the vanguard of an entire species of MechaCthulhus, is unimpressed.
Any doubt Heather had about killing Leonard Wolf in Silent Hill 3 is dispelled when it turns out he was not only an abusive father to theBig Bad, but also a giant fish person. Of course, it is later hinted that every creature Heather killed was human, no matter how monsterous, and that she had only convinced herself otherwise.
In the Ursula Vernon webcomic Digger, when the creepy figures with black wordbubbles serving a buried god are revealed to be ordinary living hyenas.
A Batman: The Animated Series episode has people being replaced by robots. Batman doesn't realize until he pushes Bullock into a spotlight and electrocutes him. The commentary for the episode even points it out.
In Teen Titans: Trouble in Tokyo, one of Brushogun's mooks is eventually revealed to just be a sentient glob of ink. Unusually for this trope, this isn't a valid excuse to kill him— Robin gets arrested for the act anyway.
Earlier in the series, the team fights armored agents of Slade, and later is shocked to find out that they're actually robots.
This references an incident early in the New Teen Titans comic book. Starfire, newly arrived on earth and before learning the language, is involved in the Titans' action against some apparent drug smugglers: she blasts them to pieces. Tackled to the ground by Robin, she kisses him and learns the language. The point was that she casually killed several minor villains, who providentially turned out to be robots.
In the 90s X-Men animated series, there were a few instances of Mecha-Mooks looking human at first, and the heroes having to pull their punches... until one got hit a little too hard, showed circuitry... and the heroes realized they could smash and bash at will. (Animated Wolverineloved discovering Mecha-Mooks, it let him act more like his comic-book self who got to slice up real Mooks.)
This was the main topic of the penultimate episode of The Secret Saturdays 2nd season when it turned out that the Saturday's Arch-Enemy V.V Argost was actually a cryptid in disguise. Not just any cryptid either. He was in fact the same Yeti who slaughtered Drew and Doyle's parents and made them orphans.
Technically, Malificent of Sleeping Beauty was never human to begin with, she's more of a dark fairy of somesort. To any rate, she does have a human-like appearance. As such, in order for Philip to kill her in the final battle, she has to be transformed into a giant, fire-breathing dragon to make it 'okay' for her to get stabbed.
Though this is more of a case of One-Winged Angel, since she's not really a dragon normally.
The Powerpuff Girls ostensibly-human enemy Roach Coach was dropped from a massive height, provoking a scared response about how its not ok for them to kill humans, then he's revealed to be an intelligent roach manning a human robot. Whom they decide to keep in a jar.