Akikan! has aluminum and steel cans (the cans are cute girls here) holding some deep prejudice against each other. The first time this comes to light is when Melon and Yell begin slinging insults at each other based solely on the material they're made out of. The fact that this type of competition is encouraged doesn't help.
In the Angel Sanctuary manga, angels are created in vitro. Naturally-bred angels are looked down upon, and outright hunted whenever they can find an excuse (the rebellion helps on that). They are often born with pale skin and red eyes, which gives them the slur name of "rabbits". This often borders on Bullying a Dragon, since rabbits are often born with extreme and uncontrolled powers.
In Armitage III, the title character is a Ridiculously Human Robot (in fact, she's so ridiculously human she can even reproduce, which is a plot point) working to investigate murders (of victims who turn out to be similar Ridiculously Human Robots) with a partner who's prejudiced against robots and cyborgs due to one causing the death of his previous partner. He is injured, and repaired with robotic prosthetics. Of course, he gets an Aesop about tolerance, and eventually marries his mechanical partner and has even a baby with her.
Probably the first & still one of the best examples in anime is Osamu Tezuka's Astroboy. Some choice examples: the robot revolutionary Blue Knight explicitly compares the robot nation he is trying to build to Israel, "The Tragedy of Bailey" storyline, where a Japanese-American cyborg brings Astro to America to try to protect the first robot to gain US citizenship from being lynched & the "Capetown Lulaby" story, which was inspired by issues of the time such as Apartheid & segregation & the latter half even takes place in South Africa. What's really strange is that the badguys from that story disguise themselves by putting on blackface.
Black Butler, intensified sixfold in the manga. Demons and Shinigami hate each other. In the Noah's Arc Circus part, William and Sebastian spend a few days and nights trash-talking each other not as individuals but as representatives of their respective races...Except for Grell, who will flirt with anything so long as it's male and sadistic.
In the Blood+ episode "Turn the Palm of Your Hand Toward the Sun", James Ironside delivers a crazed rant about the Schiffs' inferiority to Chevaliers such as himself - while trying to torture a captured Schiff to death. The scene is even more chilling because James, who is black, seems to have no idea of the terrible irony of his words and actions.
And also because his arms and the lower part of his body, which were destroyed and replaced with body parts from the Schiff, are now white. Being rejected by his capricious "mother" because of the replaced body parts is precisely what drove James (who is a fairly straightforward Renfield) insane, to boot. Even if this wasn't intended to be part of the irony, it was certainly unsettling.
Momose, a pure blooded cat demon from Bloody Cross refers to half breeds as "vulgar, barbaric and the lowest of the low".
In Bubblegum Crisis, there's prejudice against Boomers. Whether or not this influences them to go rogue varies.
Cat Soup The Cats are racist toward the Pigs. In the movie, the Cat Children mistreat the Pig who saves them and beat him to death.
In A Certain Magical Index and A Certain Scientific Railgun, several espers and the higher ups of Academy City look down on Level 0s, seeing them as worthless. Several Level 0s, particularly members of Skill-Out, hate espers, usually due to jealousy and/or being bullied. Several people from the magic side hate espers, because espers are of science.
It says a sad, sad lot about what the administration thinks of Level-Zeroes when the city's prison and graveyard is located where Level-Zeroes live.
In Darker Than Black, a man in charge of a secret operation tells the Contractor working under him, "Your whole kind is nothing more than filth, unfit to live without a patron's approval." That the man in charge is white and the Contractor black is incidental, though this possibly counts as a Lampshade Hanging.
Continued in the author's other work, Deadline Summonner. Summons are not looked highly upon by humans, and it's implied that they're little more than slaves to other summoners.
General Sakamori Miwa of Daimos is horribly racist to the Baan and wishes nothing more than to see them all killed. This culminates when he takes over Daimos and tries to kill them that way, but fails. Ultimately, Kazuya's had enough and beats him within an inch of his life before he's arrested for his crimes. When he appears in Super Robot Wars, Laser-Guided Karma hits him even more and he'll even be killed for his actions.
In Digimon Frontier, before the start of the series there was a war between human and beast Digimon which Lucemon stops. In the movie there is an island where a civil war between the human and beast Digimon there, which was perpetrated by a Digimon who can slide digivolve from human and beast forms to awaken Ornismon.
Kurata fullstop. He hates Digimon to the point where he warps Digimon data so that it can be used as a weapon to introduce genocide in a word that does not know death. Of course, this takes place before the series starts; in series, his racism just causes more genocide, medically alters people, and sets off a chain of events that nearly causes the end of both worlds.
The Saiyans of Dragon Ball Z were undoubtedly subjected to racism by Freeza and his men, leading up to Freeza single-handedly carrying out a genocide against them by destroying their planet. As we see in some episodes, the remaining Saiyans had to deal with discrimination, and being called 'filthy monkeys'.
Subverted somewhat in that Freeza's real motivation was fear, the racism was mostly a cover. He destroyed their planet because he feared a Saiyan uprising, not because he particularly hated them.
Freeza's racism is played up even more in Dragon Ball Abridged. He despises most races he encounters, but claims he's not actually a racist since he just wipes them out rather than hating them.
Kind of the point in Elfen Lied. Although Diclonii are an actual threat to humanity as a species, from what we're shown it's humans who cause a lot of the threat, combined with the simple fact that children should not have weapons.
Escaflowne's Dragon Clan are hated by almost every other race on Gaea, it is so frowned upon that the main character's Mother, makes him promise never to show his wings again, just seeing the wings of one is said to be a bad omen.
However the last part is subverted when Van's unfurled wings manages to bring the rest of the world, drunk on the power of wishing, back to its senses.
Rustyrose from Fairy Tail declares that all non-wizards are trash and deserve to die. When Elfman expresses disgust at this and says that wizards and regular people have to work together for the common good, Rustyrose calls him a fool and says that Elfman and his friends are trash as well.
Several of the demons from the Book of Zeref have a hatred of humans and want to destroy them. Marde Guille takes it Up to Eleven. When he finds out that his comrade Kyouka sadistically stripped and tortured Erza Scarlet, he brutally punished her because to him, humans are worthless and should be killed on sight, not made into playthings, and Kyouka's treatment of Erza implied that she liked her in a way and wanted to keep her.
In The Familiar of Zero, a war between humans and elves in the distant past caused both sides to consider the other evil barbarians. In addition, elves hate and fear beings who wield Void Magic and their familiars, considering them to be servants of the Devil. Tiffania really has it rough as she is a Half-Human Hybridand has Void Magic. Saito defends her and helps the others see that she is just a girl like them. Several human and elf characters have Not So Different moments.
Done in both the manga and the anime versions of Fullmetal Alchemist, with the persecution and attempted genocide of the Ishvalan people. They are visually identifiable by their red eyes and dark skin, and various characters use hats and sunglasses to disguise these traits. Several aspects of the Ishvalans' portrayal hint more specifically at a metaphorically Islamic culture: their vaguely Middle Eastern dress, Ishval's desert landscape, and their monotheistic religion and the tensions arising from its prohibition of alchemy and the Amestrians' contrasting dependence upon it.
There's also the Ishvalan prejudice or prosecution of alchemists. This is somewhat more understandable, since the alchemists were responsible for the aforementioned genocide in the first place.
Togusa of Ghost in the Shell: Stand Alone Complex has some technophobia as part of his old fashioned/Fan of the Past personality. He is initially somewhat hostile to the Tatchikomas because he bristles at the idea of their being a fully sapient artificial intelligence. In the second season, he gets set up and put through a show trial after he shoots a cyborg criminal while off duty. The main thrust of the prosecution's argument is that Togusa is prejudiced against cyborgs due to subconscious feelings of inferiority.
InuYasha has half-demons, which are hated by both humans and demons, with humans and demons also hating each other.
Though the humans hating demons aspect is generally deserved, since upwards of 90% of all pure-blooded demons are either out to kill humans on principle, or target humans for pranks or worse without consideration for the victim. Which is not to say that humans NEVER act in such a manner, just that there are some positive examples also.
Yukiji from Kamisama Kiss hates youkai with a passion, going as far as to throw parties when she hears that one of them is being hunted down. This becomes awkward when Tomoe, a Little Bit BeastlyKitsune starts to fall in love with her.
In Kidou Shinsengumi Moeyo Ken, two minor characters, a Cat Girl and a regular human man, are seen from time to time in a love/hate relationship, and then they finally decide to marry, but the man's mother adamantly refuses to allow the Cat Girl to marry him. This serves as a plot point later when Okita asks Ryunosuke's mother, Oryo, if she was okay with a half-monster daughter marrying her son. Oryo's reaction is one of shock shortly after Okita asks it, and she walks away dejectedly. Unfortunately for her, Oryo wasn't shocked at her question, but rather some cockroaches which were on the wall behind Okita, and apparently didn't hear her question. Later on we find out Oryo's perfectly okay with Okita marrying Ryunosuke if she wanted to marry him.
Kikaider had a discussed double example of this, combined with a fantastic version of Halfbreed Discrimination. A villain, who is an android in the shape of a vampire or a golden, mechanical, humanoid vampire bat, says that being an android is similar to being a bat in this respect, claiming that androids were not quite machine or human, but disliked by both and that a bat was not quite rodent or bird, but also disliked by both (the jury is still a bit out on that last one).
An episode of Kimba the White Lion has Kimba go to a lion convention only to be called a "pussy cat" for being white by the meeting's leader Specklerex and other lions. It turns out that Specklerex was jealous towards Kimba's father Ceaser for being a more successful leader than him and by the end of the episode, Specklerex developed some respect towards Kimba.
In The Legend of the Legendary Heroes, those born with Cursed Eyes are heavily subject to this. Going by some characters' personal experiences and one character's recounts of what he's seen, children born with such eyes are generally persecuted, sold to/abducted by the military, used as test subjects, and killed, often alongside their parents—if their parents weren't the ones doing the killing. Conversely, a fair number of Cursed Eye bearers are prejudiced towards humans right back.
Fate has shown some evidence of this in Mahou Sensei Negima!. Some of his internal monologues seem to indicate he doesn't consider the people of the Magic World to be real. Except for the human population of Megalosembria, they are artificial beings who will fade from existence when (when, not if) the Mundus Magicus collapses. And far from persecuting them for it, he actually claims he's trying to save them, in his own twisted way.
Marvel Disk Wars: The Avengers breaches the topic of Mutant hatred that's common with its source material. However, the kids just genuinely don't get why people like Thor (a god), Wasp (a normal human with science-fueled abilities), Iron Man (a guy in a suit) and Spider-Man (combination of accidental powers and science-y stuff) are touted as heroes and yet Mutants are regarded so negatively.
Mobile Suit Gundam had conflicts between "Earthnoids" (humans who lived on Earth) and "Spacenoids" (humans who lived in space). Closely related was the conflict between Newtypes (those with Psychic Powers, almost always Spacenoids) and Oldtypes (non-psychics, but also used as a slur for those stuck in old ways of thinking).
Gundam SEED had Naturals (normal humans) versus Coordinators (genetically engineered humans). However, the reasoning for this is muddled due to LOGOS who run a War for Fun and Profit mentality and turned the simple environmental lobbyist group Blue Cosmos into the frothing anti-Coordinator group just to rack up more money. However, it doesn't help that some Coordinators are real dicks and tend to flaunt their superiority.
Naruto: In an early arc, Haku explained that in the Land of Water the powerful and deadly abilities of clans with bloodline abilities had garnered fear and hatred from those without such abilities. The hatred was so severe that Haku's father was willing to murder his wife and son because of their bloodline.
The Uchiha in general believed themselves superior to other shinobi simply because they were Uchiha, often reflected in Sasuke's arrogance.
As such, they saw themselves as above the rest of the village and planned a coup d'etat despite being given more power than every other clan combined via being Military Police. They believed they were unjustly prosecuted and discriminated despite being a well beloved clan and the Second Hokage trusting them to have power over the other Clans. Orochimaru and Obito point out that he and the Elders forced them to live on the outskirts of the village despite 1.) Tobirama had the Uchiha headquarters on the outskirts of the village due to an already constructed prison being made there-what better facility for their appointed job? 2.) The Uchiha weren't moved anywhere during the interim between the attack on Konoha by Obito and the massacre-they had the exact same place, thus they weren't forced to the outskirts either. The Uchiha had more than enough power and even had a Hokage Candidate in the form of Uchiha Kagami (a Uchiha that Tobirama not only respected but chose as a personal bodyguard and student), were beloved and respected throughout the entire village and finally could continue to be shinobi. Orochimaru and Obito's summations shouldn't be taken seriously given they were both trying to influence Sasuke at the time. It all comes down to power, the Uchiha weren't satisfied with what they got and wanted more.
And there's also the jinchuriki, who are feared, hated, and ostracized by their home villages, or exploited and used as weapons by other people. This is a recurring theme in Shippuden, where Naruto repeatedly calls out people that insult jinchuriki.
The village, where the Uzumaki Clan lived, was attacked and finally destroyed, because their sealing techniques were widely feared.
There's the double whammy in Niea_7, where the aliens not only face discrimination by earthlings, but also maintain a kind of caste system for each other, in which lower-ranked aliens like Niea are regarded as worthless scum.
One Piece has a complicated example with the Fishmen and the Merfolk, humanoid beings that also show characteristics of an aquatic animal. Since the "aquatic animal" part is almost random and they have a lot of possible combinations, neither the Fishmen nor the Mermen discriminate against each other by distinctive traits such as their fish parts. Because of this, is perfectly normal for them that an octopus Mermaid reproduce with a shark Merman and a eel Merman be born as the result, that's also why they can't understand why the Humans classify each other in groups. But even if those species don't discriminate amongst themselves, they do discriminate against other races. Specifically, the Fishmen believe that they're superior to all other races, especially Humans, but that's also complicated because of the discrimination that the Humans have in the One Piece world against them and the Mermen as they were once considered to be on the same level as fish despite being equally as intelligent as humans.
To be fair, not all Fishmen and Merfolk believe that they're superior to humans or other races, only certain extremists, though the overwhelming majority does hate and distrust the human race.
The giants also get treated on the same level as a tank. They don't really like that. That's only really by the marines though, some are highly respected people and are treated as honorable guests.
There's also the Long-arm tribe looking for "rare people with only one joint in their arms" to put on display, or the occasional flickers of fantastic racism towards Brook (for looking like a monster) and more subtly Franky (looks like a monster without his fake skin). Basically you can be any skin color you want and no one will mind, but if you don't look human enough for the OP world's tastes things are gonna be rough.
Taken to the extreme by Hody Jones, who is is so racist that he's willing to have hundreds, if not thousands, of Fishmen and Merfolk murdered for wishing to be on civil terms with humans. This includes the much-beloved Queen Otohime, for being the figurehead of the movement. The real kicker: he flat out admits that humans have never done anything bad to him personally. He's simply internalized the Fishmen's prejudices against humans.
Done in Peto Peto San, where Japanese mythological creatures are either humanoid or have mated with humans enough to do so. The problem is averted by the series taking a lighter tone, and the solution involves something everyone can get behind, dedicating the town to "Little Sister" Moe.
Pokémon has done episodes that evoke this. One example from the Kanto episodes is "Bulbasaur and the Mysterious Garden", where Ash's Bulbasaur's refusal to evolve causes the newly evolved Ivysaur and their chief, a Venusaur, to turn on him. Another episode during Johto featured a group of Remoraid (a fish-like Pokémon) that shunned one of their clan after it evolved into an Octillery (an octopus Pokémon). Mewtwo and his army of clone Pokémon (both versions) and Mew and his army of natural born Pokemon (Japanese version only, at least in regards to Mew itself) is also an example of this.
Trip in Best Wishes often insults Ash for being from Kanto.
In Rising X Rydeen most people tend to be fearful and cautious around strangers since a lot strangers have unstable powers that can cause a lot of damage. If that's not bad enough, a good number of them use their powers for nefarious purposes.
Mikan was shunned by most of her classmates, including her best friend, when she became a stranger with electric powers and couldn't stop accidentally electrocuting things.
When students from Takara's school find out he's a stranger they immediately start gossiping about him.
Ruri's dad left her and her mom after Ruri became a stranger.
In Sekirei, some of the titular Human Aliens have very negative views on humans, referring to them as "monkeys". This varies from simple disdain to genocidal intentions. Tsukiumi starts out this way, but changes her view on humans once she meets Minato. Karasuba, on the other hand, considers humans an inferior species and wants to kill them all for being weak.
Friction exists between all of the races in Slayers: the dragons and the Shinzoku (Holy race) that serve the Gods, the Mazoku ("evil race") that serve the Demons/Monsters, and Elves all either scorn humans or manipulate them in some way or another (the first two are rather obvious, wile the Elves feel superior because they have a better innate talent with magic than many humans do). Meanwhile, most of the sub-human races (Beastmen, Berserkers, Fish-people) are either peaceful, subservient, or also scorned upon by the other three, as well as humans; the Fish-people in particular are often exploited for comedy relief. The ones that gets the worst of it, however, are chimeras.
Soul Eater has a bit of this, although it is mentioned only in passing. However, it is directly stated in Soul Eater Not! that ordinary humans fear Demon Weapons greatly, hence the law that anyone displaying those abilities must attend the DWMA until they are certified safe for society. Soul, the second protagonist, comes from an all-human family of musicians, and they were apparently "surprised" when the youngest family member turned out to be a living razor. Based on Soul's self-esteem issues related to his weapon blood, their disappointment is inferred.
Superior has humans and monsters gleefully killing one another.
In a major case of All There in the Manual, it's revealed that the Tenchi Muyo!-based alien race, Juraians, have a major thing against humans, most likely due to their "backwater" nature (seeing as humans still don't have Faster-Than-Light Travel). This is one of the major reasons Yosho (who was half-human) took off after Ryoko - he didn't want to deal with all of that and intended to send someone else in his place. Of course, his bride-to-be Ayeki, who believed Yosho was dead, was not happy to learn of this revelation.
The Anti-Spiral hate and deplore other Spiral Races, partly because of the Spiral Nemesis, but this doesn't prevent them from going on tangents that, quite frankly, wouldn't be very justified, even with the Spiral Nemesis as their excuse.
In Tiger & Bunny, it's noted that there used to be a tremendous amount of anti-NEXT sentiment, though it has lessened considerably in the past twenty years (due to the emergence of Maverick's superheroes). History of NEXT-prejudice nonetheless has an impact on the characters (both Kotetsu and Kriem grew up during this time period, and thus had to endure a lot of stigma) and on the plot (HeroTV was floundering because of it, so Maverick set up a Monster Protection Racket to keep it alive).
This trope is the core of the conflict between those with Psychic Powers known as the Mu and normal humans in Toward the Terra. Mu who are hunted down like animals. Children go through Mu tests before their final maturity exams and are immediately exterminated, if the results are positive. These ones who managed to survive have to hide in a stolen starship in higher layers of atmosphere. The whole mess ends with the Mu forced to leave their home planet and flee across the galaxy. Later the ones, who become racists are some Mu themselves - against humans and against some of their own kind.
The Plants in Trigun are conscious beings that humans exploit for power, resources, etc. Though to be fair, most humans don't know that the Plants are even alive, let alone sentient.
A major theme of Trinity Blood is that vampires and humans can and should stop fighting and live in harmony.
The battle of ESPers vs. "Normal People" in Zettai Karen Children is one of the underlying themes of the series. Almost all of the ESPers in the series are under the watch of the government, and it's shown that when someone is discovered to have powers, they're treated harshly for it. Good thing Minamoto serves as Morality Chain to The Children.