A Fox Tail has racism between foxes and wolves, particularly since the main couple are a fox and a wolf. There is a powerful lobbying group known as the "Association for Fox Rights" which develops a fox-supremicist splinter group who attempt to assassinate Vulpie for marrying a wolf (and making their species look bad by hacking everything).
Extremely pervasive in the Age of Fire Series. Most humans and elves hate Dragons, dwarves are divided among those who hate them and those who see them as potentially useful Dragons tend to see most other sentient races simply as food. There's also, in the first book, an increase of racism towards dwarves and elves by humans.
The Algebraist by Iain M. Banks. AIs lose a Robot War against their fleshy friends. The survivors in hiding are reviled as abominations with parallels of religious bigotry and racism. As the story progresses the AIs are implied to be most unlike the Killer Robot stereotype and the "war" begins to looks more like Kristallnacht.
In Amtrack Wars series there is considerable prejudice on all sides between humans and Mutes. On the human side it is varied. The Federation considers the only giood Mute to be a dead one while the renegades and Iron Masters are willing to trade with them but still look down on them.
There's a lot of racism directed at Andalites in Animorphs by the Yeerks, who see them as arrogant meddlers of the galaxy. Most other species are openly hostile to the Yeerks, for understandable reasons.
And the Andalites themselves are eventually revealed to deserve a lot of that disdain; they see humans as so far beneath them that they decide to destroy the Earth after letting as many Yeerks as possible crowd onto it, and one book centers around how an Andalite who's lost his tail blade is seen as worthless.
In Laurell K. Hamilton's Anita Blake series there is considerable prejudice against both vampires and weres, and in some cases between lineages of vampires and species of lyncathropes (for example, werewolves regard wererats as inferior, some weretigers aren't too fond of any other species or even those fellow weretigers who aren't a purebred color, etc). One character develops a near murderous prejudice against vampires when his son becomes engaged to one and being infected by lycanthropy will generally get you fired if you're a teacher or in the medical profession even though it's technically illegal to.
As of The Atlantis Complex, we see Turnball Root commenting on how the fairies are wasting resources to the point of throwing away something that would have only taken a dab of silicon gel to fix. The fact that it's also a mastercomputer of a space probe makes this an example of bad security as well.
Fantastic races is one of many features that makes China Miéville's Bas-Lag novels as fun as it is. Prejudice against non-humans is institutionalised, inter-species romance is seen as a perversion, and the Remade (people who've been freakishly transfomed as a punishment) are pariahs who are used as expendable slaves.
Done with a twist in Kit Whitfield's Benighted in that what we would regard as normal humans are a despised minority in a world of werewolves.
In The Berenstain Bears' New Neighbors, a panda family (who are implied to have immigrated from China) have arrived at the Bears neighborhood. Although Mama Bear and the kids are okay with them, Papa Bear isn't. He also goes so far as to keep his kids away from them, and claims that the "posts" that their neighbors are setting up are a spite fence. In actuality, it was bamboo stalks for their dinner. All warm up to them by the end of the book, and enjoy their bamboo.
In Vladimir Vasilyev's The Big Kiev Technician, all "fantasy" creatures look down on humans, whom they consider too short-lived (which they are, comparatively). On the other hand, some of them recognize that this causes humans to be more creative than those who are stuck in the old ways. The protagonist proves them right. Additionally, it's revealed that there is a small group of humans called Longers, who can live for several centuries but are otherwise human. When humans in Big New York found out that there was a small community of Longers living among them, they slaughtered the "freaks", even though they have never displayed such outright hate for non-humans. This is explained by the protagonist's Love Interest (who is a Longer, as is he, even though he doesn't know it) as hitting it close to home that there are beings out there who will live for much longer than you'll be alive.
In Black Crown, the northern tribes are regarded by the south as little more than dangerous barbarians.
In Samantha Shannon's The Bone Season there is considerable government fostered hatred towards Voyants, people with Psychic Powers. They are outlawed and if caught they are either executed or "disappeared" unless they choose to work for the government rounding up their own people.
Additionally, the voyants who are captured by the government are sometimes sent to a penal colony run by a magical race known as the Rephaim. Most Rephaim despise humans and are required by their ruler to wear gloves at all times to prevent touching them directly.
In The Books of Beginning, the young hero Michael Wibberly has gotten all of his knowledge about both dwarves and elves from a book titled The Dwarf Omnibus, which was written by a dwarf, and thus has come to believe that all elves are lazy, stupid and vain. In the second book of the series, The Fire Chronicle, he is forced to re-examine his beliefs when he actually meets some real elves and discovers that while they may certainly be vain, they can also be very courageous, dedicated, and good to have on your side on a fight.
The Boundary's Fall series exhibits this in spades - the magically Gifted look down on "the commons", the commons fear and resent the Gifted; the Elves view the Garu'nah as wild savages and Humans as just plain inferior, and the Garu'nah think the Elves are honorless and arrogant.
Kate Constable's Chanters of Tremaris series see its character throw this around a lot: non-magicians largely hate the Chanters; whereas priestesses of Ice-Call see themselves as superior for protecting and cherishing their Magic Music; the mute Tree People hate the Voiced Ones for an ancient war that almost wiped out the former but also hate Halasaa, who possess their hereditary magic both for his powers and for being part Voiced One.
In David Gerrold's Chess with a Dragon, human beings are treated with open contempt by other sentient species, for being mammals. Most sentient races in the galaxy evolved from dinosaur- or bird-analogues, and consider mammals to be revolting vermin, if not bite-sized snacks.
Monsters look down on humans in City of Devils, referring to them as "meatsticks."
Because the titular human society is so militaristic and xenophobic, this trope is everywhere in Codex Alera. The Marat are usually called barbarians, are constantly said to have sex with animals, and eat people (although depending on how you read it, both the first one and definitely the last one turn out to be actually true). On the other hand, the Alerans are also prejudiced against the Canim and the Icemen, both of whom are far more complex than humans depict them.
Of course, both the Marat and the Canim are also hideously racist against the Alerans. A large part of the Aleran speciesist views stem from being the descendants of a Roman legion stranded on a world full of hostile monsters. The only group that really gets off well in this is the Icemen, because the Aleran-Iceman conflict is really nobody's fault.
Despite having demon and vampire friends, as well as a were-fox girlfriend Colt ReganHates Were-rats.
In Courtship Rite, although half of the Kaiel clan are creche-born children of uterine replicators, the creche-born are considered somewhat second-class citizens. By the rules of the clan, Hoemei should be the next Prime Predictor, but because he's creche-born, there's some question about whether it will be allowed.
In Harry Turtledove's Darkness series, an allegory of World War II set in a fantasy world, the nonsense of prejudice is put front and center by making those with Aryan features (their oppressors call them "the blonds") the equivalent of Jews (the Polish analogues are the ones with more typically Jewish features). He also does this in War Between the Provinces, essentially the same thing for the Civil War with blond serfs as the equivalent of southern slaves.
The trailmen and catmen in the Darkover series are the frequent targets of bigotry by the humans.
Dwarves mistrust elves in Katharine Kerr's Deverry series. Their main belief is that the elves are all thieves, and go as far as placing enchantments on their own metals that run with light if an elf (or even a human with elven blood) touches it. Otho the dwarven silversmith removes the enchantment on Rhodry's silver dagger so that he can pass unnoticed, as a favour to Jill.
Humans also enslave The Old Ones who were one of the original races of Annwn before the humans arrived.
Averted, mostly in Dirge for Prester John. John is terrified of Pentexore's inhabitants, but he warms to them over time. Other humans don't react so well when John leads them out into the world. The races of Pentexore themselves don't feel this towards each other. Unless you count the people on the other side of the diamond wall.
The Discworld books have always done this skillfully, using it, subverting it, and double-subverting it.
Especially interesting is Commander Samuel Vimes of the City Watch. A self-described speciesist, Vimes has nonetheless allowed the Watch to become one of the most species-blind employers in the city, and recognizes better than most the value of its non-human members, such as dwarfs, trolls, and even vampires, for whom he still harbors an innate and intense dislike. Mind you, Vimes is also a big-time misanthrope, so his dislike tends to manifest in his policeman's tendency to treat everyone as a vicious bastard until proven otherwise. Vimes himself says to a dwarf recruit "I don't like dwarfs much, but I don't like humans much either, so maybe that makes it okay, I don't know."
The Discworld includes its own racial epithets equivalent to our N-word: "rocks" for trolls, "lawn ornaments" for dwarfs, etc. The trolls have "squashies" for humans.
Pratchett also depicts non-fantastic intra-human racism in Jingo, with Morporkian bigotry against Klatchians and Klatchian bigotry against Morporkians. The warlike, nationalistic motive behind the racism is very bald, with self-contradictory propaganda about Klatchians being both brutally violent and contemptibly cowardly. Fred Colon tries to pull a "can't trust them dark-skinned folk" to justify his hatred for Klatch, which is discredited when Nobby points out that Omnians are pretty brown and Fred has no problem with them.
Non-human species often show a lot of Fantastic Racism toward each other, as well, most prominently the conflict between dwarfs and trolls. Werewolves and vampires also have a long history of mutual disdain.
There're also racial pecking orders within species.
Trolls from sedimentary families are considered lower-ranking those from igneous families. Thud! shows us the two extremes of the geology-based class system: at the top is the Diamond King (although Mr Shine is too enlightened to hold such prejudices himself), and at the bottom is Brick.
Dwarves have complex cultural standards for what makes one a "real" dwarf. Carrot considers himself fully Dwarfish despite being biologically human and there are plenty of dwarfs who actually agree with him. On the other hand, Ankh-Morpork is now the single largest dwarf population center, but many "deep dwarfs" consider anyone who leaves the mines to live among humans to have Gone Native in the wrong direction. The fundamentalists of Thud! think even speaking to humans is a sin.
There is a conversation in the novel Men at Arms in which prejudiced nobles simultaneously treat dwarfs as inferior and yet fear their cleverness and cunning, with the hypocritical logic of antisemitism or xenophobia. This book's Captain Quirke probably shares the title of "most deeply bigoted human" with Lord de Worde from The Truth.
In Snuff it seems that everyone looks down on goblins.
Dwarves give us a rare version of fantastic transphobia. Dwarves are outwardly a One-Gender Race; while there are both males and females under the armor (in fact, 90% of dwarf courting is working out whether the object of your affection is of the opposite sex), everybody is expected to act masculine. At least until some female dwarves like Cheery Littlebottom come to the big city and start to like all this stuff about lipstick and dresses and being a girl. After a lot of resistance, she gets to change her name to Cherry/Cheri and is officially recognized as a woman. There are hints that the current Dwarf King is in fact female.
In the Disgaeanovels the demons care much more about race then in the game, and worst example is Laharl’s aunt Yasurl who justifies violently abusing her nephew because of his half human blood and tries to have him assassinated because she thinks his blood makes him unworthy of being Overlord.
The wars between the various "monster" cultures of the web-novel Domina subvert this a bit. While angels hating vampires who hate kemos sounds like its this trope (and Mr. Exposition describes it as such), The Rant mentions that it's more like a gang war.
In Dora Wilk Series most angels consider other races inferior, demons hate devils for bossing around, angels and hellians despise magicals and vice-versa (Inquisition, anybody?), vampires dislike werewolves for being barbarians, vampire lords consider everyone else as snacks, werewolves believe magicals want to enslave them, magicals don't like vampires because they suck blood and werewolves because they're mostly criminals, she-devils have terrible reputation throughout the rest of magical world... and let us not even begin on the subject of half-bloods. Frankly, half of the plot is driven by Fantastic Racism.
In the Dragaera novels, the Dragaeran treatment of Easterners calling to mind human racism and ghettoization of minorities, and the Dragaeran prejudice to Dragaerans descended from multiple Houses calls to mind various "purity of race" prejudices on Earth.
Weiss & Hickman's Dragonlance has tons of this, the most readily available example being Tanis Half-Elven, he is accepted by neither his human or especially his elven kin at large. It seemed like nothing short of saving the world would allow him to be accepted by the humans, even after that most elves, save his wife, still can't stand the thought of him.
In The Edge Chronicles, there is occasional mention of mistreatment and suspicion being directed against the Slaughters, a race of crimson-skinned, red-haired, nocturnal humanoids. Except, as the first book reveals, despite their ominous name, appearance and habits, the Slaughters are in general very decent people. Their name comes because their racial hat is their knack for butchering livestock and preparing meat, leather and other animal by-products that they then sell to the other races at the various trading markets. They sleep all day because butchering and tanning are hot, hard work and it's easier to do so in the dark. The red skin and hair is just a case of Astonishingly Appropriate Appearance.
David Eddings' The Elenium/Tamuli books feature Elene contempt for Styrics (verging on medieval attitudes towards the Jews). The Styrics in turn detest the Elenes (with good reason, considering past atrocities) and the Delphae. Just for fun, people in the subject kingdoms of the Tamuli empire refer to their rulers as "godless yellow dogs" (a vile slur; as Oscagne points out, "We have gods. Give me a few moments and I might even be able to remember some of their names"). The distinctly Nazi-esque Cyrgai consider everyone inferior. And, to extend this a bit further, trolls don't like being called ogres.
An important part of the ending of the original novella version of Enemy Mine, with humans and Drachs continuing to resent and look down on each other even after the war is over such that the lead character rescues his adopted Drach son from an insane asylum he had been put into due to his ties to humanity and goes back to the planet he was originally stranded on to create a colony for people who were willing to get past it.
In Fates Road, the carriors are shunned because they will one day turn into creatures. Also, Ron Frazier's hatred for the creatures is his sole motivation for everything he does.
In C. J. Cherryh's Foreigner series, the conservative humans against the alien atevi, and visa-versa. On the human side the conservative humans think that the atevi are entirely to blame for the disastrous War of the Landing. On the atevi side the conservative atevi: 1) think the War of the Landing was the fault of the humans, 2) are traditionalists who hate the technology the humans have brought (and the cultural changes which came with the new technology), and 3) resent that one atevi region and ethnicity, the Ragi, have become so powerful because of their alliance with the humans.
In Glen Cook's Garrett, P.I. Garrett admits to hating ratpeople, a prejudice shared by most of the folk of Tunfaire, the city in which most of the novels take place. However, his attitude changes after his close association with ratwoman Pular Singe. Originally hired as a tracker (ratfolk have a phenomenal sense of smell), Singe impresses Garrett with her intelligence and personality to the point where she is now a full partner in his professional endavors. She also manages his budget.
Speciesism is a major plot point in one Garrett book and keeps recurring in later works. After a decades-long war ends and human veterans return to the city, they find that most of the jobs back home have been taken by nonhumans (humans have to serve; other races are exempt). This leads to the creation of The Call, a "human rights" organization dedicated to the eviction or elimination of dwarves, elves, half-elves, ratfolk, ghouls, gnolls, and exotics (apparently, non-humans have no qualms about inter-species romances—"exotics" are people whose ancestry is not readily apparent) from the kingdom.
In Generation Dead, teenagers all over America are coming back from the dead. Some are just like regular teenagers, only slower talking and with a lower body temperature. Others are very slow and can barely walk. The "zombies" are every minority that ever existed combined. How they are treated is almost like how black people were treated in the Deep South. The high and low functioning is almost like mental retardation. The series even arguably addresses discrimination against AIDS sufferers in the early 80's with the death of Adam Layman, who was considered an all-American pillar of the community. When he comes back as a zombie, he is treated with scorn and disgust similar to that of one of the most famous AIDS sufferers, Ryan White.
In Sergey Lukyanenko's Genome, the Specs and the Naturals have a deep-seated distrust of one another. The Specs consider themselves superior to the Naturals, while the latter see the Specs are freaks. The novel doesn't mention any actual violence towards either group, though. When the main character, a Spec, is hiring crewmembers for his ship, a man offers his services as a skilled navigator. He first asks if it is a problem he's gay, which causes the protagonist to be offended by the assumption, as this sort of discrimination is completely gone by that time. The navigator then adds that he is a Natural, which almost immediately causes the protagonist to want to reject him, but having just said that he's beyond petty prejudice, he can't go back on his word. This was the nagivator's plan all along. He later tries to find any flaw to use as grounds for termination, but the Natural proves himself to be an excellent navigator.
The navigator himself has an irrational hate towards clones, which Imperial law recognizes as human beings. Many humans also have problems with aliens, especially the people of Ebon, who believe it is their divine mission to rid the galaxy of aliens to make way for the "true children of God".
In Line of Delirium, another of Lukyanenko's novels, clones and genetically-engineered humans are illegal in the Human Empire by order of Emperor Grey (who isn't actually a tyrant, just a regular guy with regular prejudices). So, naturally, the two protagonists are a clone and a genetically-engineered "super".
In Go, Mutants! there is a lot of prejudice against both aliens and mutants. This is encouraged by the government.
Quinn at his lowest points resorts to actual racism, usually against Edilio. In fact, nearly every villain refers to Edilio as "the Mexican". Lampshaded in the second book by Edilio himself:
Edilio: "I'm not just your good-looking Mexican sidekick."
Sam: "You're not Mexican, you're Honduran."
Edilio: "Sometimes I forget."
In Plague, Lance goes full-out racist and blames blacks, gays, Mexicans and Jews for all his problems, as well as freaks.
The science fiction novel "The Green And The Gray" by Timothy Zahn focuses on two not actuallyHuman Alien species called the Gray and the Green, secretly living among humans in New York, who fought in a terrible war on their actually Earth in the distant past homeworld, fled in two starships to Earth and assumed the other had died in the genocidal conflict. They land in 1920's New York within days of each other, and the human immigration officer on Ellis Island that they both use assigns them to opposite sides of the city, hoing they'll never find out about each other. It has a lot of paralels to ethnic conflicts, imigration and assimilation into American culture.
Zilpha Keatley Snyder's Green-Sky Trilogy deals extensively with the tensions between the fair-skinned, tree-dwelling Kindar and the darker-skinned, underground race of Erdlings. In this case, the difference between the Kindar and Erdlings was as much cultural as ethnic (The Kindar were vegetarians and the Erdlings hunted; the Kindar believed in repressing all negative emotions, while the Erdlings were very expressive. Among other things).
In the Griffin's Daughter trilogy, half-elves get it from both sides: The elves consider half-elves (or hikui, in the elves' language) second-class citizens, akin to African-Americans during the first half of the Twentieth Century. Humans consider half-elves advanced animals at best, abominations at worst. Not that humans and elves see each other much better: Elves see humans as rapacious barbarians. Humans (or at least the human kingdom in the story) see elves as creatures of evil, looking to steal the souls of men.
Some "pureblood" wizards look down on Muggles and those who have Muggles in their ancestry. Draco Malfoy displays this often, calling Hermione a "mudblood" more than once (a slur for a wizard or witch that is born to non-magical, aka "Muggle" parents, who "purebloods" of certain persuasions, like the Malfoys, see as inferior) and such insults almost always end up badly for him, since the wizard m-word is as nasty as the muggle's n-word.
The larger theme of non-humans being discriminated against. The "official" wizard attitude to the other magical races is clearly portrayed as a different kind of racism to the Nazi-esque Death-Eaters, not open-minded egalitarianism; Harry is surprised to see a statue at the Ministry of Magic with a centaur and a goblin in submissive adoration of a wizard and witch; totally preposterous (unlike the house-elf in the same statue), but evidently the way the Ministry believes the world "should" work.
Dolores Umbridge hates centaurs, and Firenze the centaur gets into trouble with his own people, who consider him an "Uncle Tom" and traitor for associating with humans. The Ministry of Magic classifies all living creatures as either "beast" or "being", with the latter being less discriminated against. Centaurs are classed as "beasts", and thus discriminated against greatly... because they themselves discriminated, and weren't willing to share "being" classification with things like vampires. According to tie-in materials they were also insulted that humans thought they had authority in such matters at all, and originally insisted on the beast classification after the mermaid civilization was filed there for not speaking English (which was later rectified).
There is anti-werewolf legislation that makes it very difficult for werewolves to gain employment. Lupin chooses to resign from his teaching position after everybody finds out he's a werewolf, arguing that parents would not want a werewolf teaching their children. He also comments that most people find it very difficult to speak to him once they find out what he is.
The treatment "halfbreeds" who have one human and one non-human parent, such as Hagrid (a half-giant).
Hermione's well-meaning campaign on the behalf of house elves. In The Half Blood Prince, Tom Riddle murdered a woman for her artifacts and framed her house elf for it. Dumbledore tells Harry that the Ministry should have investigated further but didn't "...because she was a house elf". Harry had never sympathized with Hermione's campaign as much as he did at that moment. However, Hermione's campaign is portrayed as well-meaning but misguided, with her imposing human values on the elves and refusing to accept that the vast majority of them are actually happy with their jobs as long as they're not abused. She seems to have become better educated on the house-elf psyche by Harry Potter and the Deathly Hallows, though, and has gone for a more practical approach—at no point in book seven does she ask Harry to free Kreacher, but she does convince Harry to treat Kreacher well despite his betrayal in Harry Potter and the Order of the Phoenix. It pays off almost immediately, and again at the end of the novel.
The Dursleys are very bigoted against wizards.
Squibs (non-magic children of witches and wizards) are largely looked down upon. Even the Weasleys have a relative (Molly's second cousin) who possibly is a squib and, as such, an embarrassment to the family.
Kim Harrison's The Hollows series has a broad and increasingly obvious undercurrent of fantastic racism that can be traced back to a fantastic Holocaust between the Demons and the Elves that's still playing out in a kind of slow motion disaster for all sides.
In the Honor Harrington series, the use of genetically-modified troops during Old Earth's Final War has led to widespread prejudice against genetically-modified humans ("Genie" is sometimes cited as an in-universe slur against GM humans, though it rarely actually appears in dialogue).
It never occurs to the souls (including Wanderer, at first) that maybe they shouldn't be taking over the minds of every species they run across and essentially wiping them out. One species commits mass suicide to escape them; rather than rethink their system the souls cheerily continue infesting the ones who didn't escape in time, pausing only briefly to regret the waste of host bodies. They also tend to babble about humans being violent, while at the same time making an organized effort to "discard" all "wild" humans.
Even after Wanda comes to the conclusion that Humans Are Special and shouldn't be hosts, she doesn't extend the same consideration to the other species that the souls have conquered. For that matter neither do the humans, who are more than happy to ship disembodied souls off to other worlds to inhabit hosts there.
The Seeker, at atleast in the film, makes a point to mention that Earth is the only planet that they have done this on where the inhabitants were not symbiotic with the Souls.
All over the phlace in the Inheritance Cycle, where all sentient races display varying levels of prejudice towards each other:
Everyone hates the Urgals, a race who have a rite of passage that demands that the young must find something, anything, and kill it. Everyone else sees them as utter barbarians, which to a certain extent is true, but their culture is actually a bit more complex than simply fighting and killing. Eragon has a discussion about this with one of their leaders.
Eragon:"You've killed many humans haven't you?"
Nar Garzhvog:"And you have killed many Urgralgra."
Nobody really likes the Elves either, seeing them as creepy, arrogant jerks. At the same time, everyone respects them, because they are physically and magically superior to the other races.
By extension, the Elves really are arrogant bastards, and more or less look down on everyone. Beside the Urgals, they see the Dwarves as superstitious fools and humans as rough barbarians.
Frankly, the only races who aren't overtly prejudiced toward each other are humans and Dwarves, who get on pretty well.
In R.A. Salvatore's The Legend of Drizzt, most of the people react either with fear or hostility upon meeting Drizzt Do'Urden for the first time. This isn't surprising since dark elves don't have a very good reputation, but even after people realize he isn't out to cause trouble like most of his kin, they often still shun him.
In Just a Little Different from the Little Critter books, there is a turtle/rabbit kid that most of the other children don't want to play with because he's "too different." This makes Little Critter angry, however, and he decides that the new kid isn't too different to play with him. Eventually, he manages to convince the other kids as well.
The Last Dragon by Silvana De Mari has what amounts to concentration camps for elves, who are so mistreated that they eventually nearly die out. The main character of the book is the last elf.
In Malazan Book of the Fallen by Stephen Erikson this is a frequent theme. Seven Cities and the Malazan Empire; Letherii and Tiste Edur; Letherii and Awl; Bargast and Moranth; Tiste Andii, Tiste Edur and Tiste Liosan all hate each other; Imass and Jaghut, Jaghut and K'Chain Che'Malle, K'Chain Che'Malle and K'Chain Nah'Rhuk, the Tiste races and K'Chain Che'Malle. Basically, everyone hates pretty much everyone else.
The Mediochre Q Seth Series has examples against dragons, who (despite being sapient) have been hunted almost to extinction, and the undead.
Nobody gives mundanes any respect in The Mortal Instruments. One of the more blatant examples was when Simon takes down the Greater Demon in City of Bones. An Amazon.com review notes that the Shadowhunters react in a manner that "suggests Simon's mundane status was a crippling retardation he managed to overcome; apparently mundanes are incapable of dexterity, motor skills, or strategy?" Who was making weapons before the Nephilim were created, again?
Not just mundanes, but Shadowhunters in general tend to look down on Downworlders too, and the vampires and werewolves are constantly at each others necks, and the Faeries are equal-opprotunity misanthropes.
The elitism of the Shadowhunters is often Lampshaded by outsiders, notably Clary and Simon, as well as Downworlders.
Every single race of humans in Nerve Zero despise one another, to say nothing of how they view those of mixed blood.
In his A Shade of Grey the society in the book is divided along lines of what color of the spectrum is visible to you with Purples being highest, then Blues, and so on with those who are completely colorblind, Greys being the lowest.
His Thursday Next Series has discrimination against Neanderthals - they have been cloned and are therefore considered the property of the company who did it.
In the October Daye series Pureblood Faerie look down deeply on Changelings. This is a running theme throughout the series.
In Jack McDevitt's Chindi (part of his Priscilla Hutchins series), it's mentioned that stealth studies of the winged aliens of the planet called Paradise reveal that the initial landing party was probably attacked because the natives consider a lack of wings to be a mark of evil.
In Red Handed by Gena Showalter, humans and aliens (or Outers, as they are called) don't get along and aliens are even hunted. This is explored more in the companion book, Blacklisted.
The hailene from Rune Breaker hate any hailene half-breeds or hailene who just happen to not have appropriate wing or hair color, dubbing them ang'hailene or 'not people'. The main character Taylin, an ang'hailene, in turn struggles with her racism against hailene and wariness at minotaurs, who she fought when she was a slave.
The other races in turn view all hailene as narcissistic warmongers.
There's also some question of if another character, Brin is racist against miare.
The Seven Realms Series has this everywhere and it's even justified at times! The Demon King, the man said to have nearly destroyed the world 1000 years ago, was in fact, a wizard. Upon his defeat, the Spirit Clans stopped making extremely powerful amulets for the wizards to use (this alone making the wizards think lowly of them), but it was forbidden for a wizard to ever marry the ruling queen. On top of that, many peoples throughout the seven realms think of the Spirit Clans as savages and wizards as heretics. The ill-will between these peoples really make things more complicated for the heroes later on in the story.
In Adrian Tchaikovsky's Shadows of the Apt series there is considerable tension between the magically oriented Inapt races and the technologically oriented Apt ones. Much of this comes from the latter having been the former's slaves before overthrowing and eclipsing them. Also Mantids and Spiders hate each other, even though they are both Inapt for reasons both have forgotten. Likewise Moths and Butterflies. Meanwhile any Ant will distrust another Ant if they're from a different city-state, Wasps look down on everyone else and everyone looks down on half breeds.
Dr. Seuss' story "The Sneetches" is a thinly disguised allegory on racism (or classism). It describes a conflict between two subgroups of the titular Sneetches, a race of bird-like humanoids. One group has stars on their bellies, and thinks themselves superior because of it, while the other group doesn't. The Aesop comes after a huckster with the unlikely name of "Sylvester McMonkey McBean" convinces those without stars to pay him to have stars added to their bodies. Then it's no longer so special, since everyone has stars, but McBeen has a machine to remove them as well, for a modest consideration. The two groups proceed to repeatedly alter who has stars and who doesn't, along with which of the two conditions are more desirable. By the time McBean packs up his operation and leaves, they don't remember who had stars to begin with and who didn't, and thus abandon their prejudices as worthless.
Absolutely slaughtered in Tom Holt's book Someone Like Me. Humans and monsters in a post-apocalyptic Earth have been fighting and killing each other because each sees the other as evil. Told entirely from the human point of view, the novel ends when the protagonist finds that one of the monsters knows how to talk, and is just as human as he is. However, he kills it anyway, because he'd been killing them for so long he wouldn't be able to face thinking of them as people.
In The Sookie Stackhouse Mysteries, there are several forms of racism. All the supernaturals think they're the best, and better than just plain humans, so there is segregation along supernatural lines:
Vampires think they're better than Weres, Shifters, Faeries, and Witches.
Weres think they're better than Shifters (Shifters don't turn into wolves. Weres only turn into wolves) and think Vampires are disgusting, to the point of slurring humans who associate closely with vampires. Shifters call themselves Weres when the wolf-type two-natured can't hear and think the wolven lycanthropes are thugs.
As you get to know the fairies, farther on in the series, they are shown to be prejudiced against anybody not-fairy. They're divided into two factions, one wants to kill all part-fairy hybrids.
Witches have infighting between Wiccans and nastier factions, who abuse vampire blood like normal people abuse drugs.
Humans are prejudiced against vampires, thinking God likes them better. And also because Vampires, y'know, eat them.
In Spock's World, many Vulcans don't respect or like humans, seeing them as little more than animals.
In the Star Wars Expanded Universe, racism between humans and nonhumans, and between different species of nonhumans, sometimes comes up. The first kind is especially prominent in parts of the X-Wing Series, where the nonhumans living in an alien's slum decide that a Rebel plotter's refusal to dance with one of them means that he is speciesist and can be killed as an example, despite sitting at a table with other nonhumans who defend him. Plots to exploit the unease between species pop up a lot in the more cerebral Star Wars novels.
Oppression of non-human races was a stated part of Imperial Doctrine. Near-Humans got off a lot better, but not perfectly.
Less mentioned is the plight of droids, ranging from mere automatons to thinking, feeling beings, all of them property with memories that can be wiped at a whim. It rarely comes up.
Then there's some mild prejudice against cyborgs. A prosthetic eye or hand is one thing, but it seems like the more mechanical someone is, the less of a future people regard them with. Ton Phanan epitomizes this feeling.
In Vision of the Future, this conversation between Han Solo and a clone of BaronFel. At the time, no details about the Clone Wars were known, and Zahn like most other authors assumed that the clones hadn't been on the Republic's side, so the antipathy was a bit different in origin.
Han Solo: So what's it like being a clone? Carib: About as you'd expect. It's the sort of secret that gets heavier with time and age. Han Solo: Yeah. I can imagine. Carib: Excuse me, Solo, but you can't possibly imagine it. Every time one of us leaves this valley it's with the knowledge that every outside contact puts our lives and those of our families at risk. The knowledge that all it will take will be one person suddenly looking at us with new eyes, and the whole carefully created soap bubble of the ever-so-close Devist family will collapse into the fire of hatred and rage and murder.
The Yuuzhan Vong consider themselves the Master Race, and declared a war against everyone else to wipe out the galaxy's "impurity". They doubly hate technology-users.
In David Sedaris' Squirrel Seeks Chipmunk, racism in the animal kingdom is touched upon several times, notably in "The Squirrel and the Chipmunk", in which a female chipmunk's family disapproves of her squirrel boyfriend; also in "The Cat and the Baboon," "The Toad, the Turtle, and the Duck," and "The Parrot and the Potbellied Pig," in which characters make inadvertent "speciesist" gaffes.
The Firbolg of Symphony of Ages are a primitive and largely-savage race. Although their reputation as brutish and cannibals is well-earned, they are also intelligent and have a strong internal society. Despite this, other races have largely regarded them as monsters to be driven back.
The most telling example of this racism was a practice of a human kingdom bordering their territory referred to as "Spring Cleaning". Every spring the ruler would mount a punitive expedition into Firbold land and raze any villages discovered to the ground, leaving few to no survivors. As pointed out by another character, the Firbolg had not launched even a retaliatory raid within the lifetime of the lord or his father.
In Tale of the Troika, Gabby the Talking Bedbug is a Bedbug supremacist, who sees humans as an inferior species.
Explored in depth in the Temeraire series, where dragons are treated by most Europeans as nothing more than quite intelligent pack animals or weapons platforms. People will casually discuss breeding dragons for various traits, and even whether or not it would be a good idea to slaughter all feral (riderless) dragons - all this despite the fact that dragons can speak English (and often several other languages) extremely well and have a normal human range of intelligence. In this case, it's almost not even a metaphor for anything, because the books are set during the Napoleonic era, with all the racism and sexism of that time fully intact. After all, if people can decide that Asians, Africans, and women are inferiors, how much more a non-human intelligence?
You mention the ferals, but not the plan to send a dragon infected with a disease that kills dragons horribly over to France and let the disease wipe out not only France's fighting dragons, but those in the breeding grounds too, AND thousands of others outside France too — Don't worry, Laurence and Temeraire bring them the cure.
The Rings of Saturn has normal people, fearing for their jobs, prejudiced against cyborgs. Not that the 'borgs are that innocent themselves. In fact, pretty much every single cyborg encountered in the book just happens to be a dangerous criminal.
In Time Scout, persons with indeterminate genitalia or intermediate gender face discrimination. The response of some to "intersexuals" is well over the top. However, they may be vamping for the camera to help paint someone as a villain.
In Kim Newman's "Tomorrow Town", a group of 1970s futurists have set up their community as a projection of the year 2000 will be like (in their estimations at least). They claim to have 'evolved' beyond many of the divisions and problems faced by people in that time period, but at one point a member of the community makes a sneery comment to one of the outsider detectives in town to investigate a murder, calling him a 'yesterday man' in the heat of the moment. The detective calmly but pointedly notes that she's been very careful not to use that term around him, the clear implication being that it's a slur towards people who aren't as similarly 'evolved' as they are — yet more evidence that their vision of the future isn't quite as perfect and 'evolved' as they like to think.
The vampires, including the Cullens, are strongly prejudiced against humans. Bella accepts fairly easily that vampires are superior to human beings, never wondering why, if this is true, that the Volturi are so dedicated to keeping a supposedly inferior species from finding out about the handful of vampires in the world.
Even though the crawlers/cockroaches, gnawers/rats, spinners/spiders, fliers/bats, etc. that coexist with humans in the Underland are not human, they are sentient and treated as full characters on the same level as humans. Prejudices held among human characters towards these species are even treated as equal to any intra-human bigotry.
The bats, humans, and mice are allies with each other, and hate the rats, who hate just about everyone but especially the humans and mice. The insects pretty much hate all the mammals. The spiders are willing to play both sides, and the cockroaches are considered stupid.
Vikus is one of the few Underland humans who doesn't have it.
Like Luxa, Henry mocks the cockroaches and even attempts to kill Ripred although this was more because of his alliance with the rats.
Un Lun Dun features largely irrational racism between living beings and ghosts, specifically, the ghosts supposedly steal bodies. Woe to the only known half-breed: everybody mistrusts him. All the more noticeable as the inhabitants of the eponymous city otherwise display extraordinary diversity and tolerance.
In Dani and Eytan Kollin's Unincorporated World series artificaial intelligences, known as "avatars" hide their intelligence from humans for fear of exactly this. When it becomes known one faction launches a war against humanity.
This is the central theme in the novel Vampire High, which is about a boy whose family moves to a small town where about half of the inhabitants are Friendly Neighborhood Vampires who call themselves jenti. The town is very self-segregated, with an unspoken rule that humans will not go in to 'jenti' stores and vice versa. After getting kicked out of the public school, he ends up attending the jenti school because vampires will die in water and the school needs a water polo team.
One of the most important plot devices of Vorkosigan Saga. Word of God says that the author pondered "What is the meanest thing I can do to my hero" and then answered, "Make him a cripple on a planet that has a murderous Fantastic Racism toward cripples". On the other hand the series is set at a time when that sort of thing is becoming more muted at least among the upper classes of Barrayar, Miles is protected by his father's status, and anyway his friends and faithful armsmen don't seem to mind.
The aforementioned prejudice is principally a result of Barrayar's peculiar history. Very shortly after the planet was settled, the only wormhole connecting the system to the rest of the galaxy collapsed, and Barrayar fell into a near-medieval state, and for centuries its populace were right on the edge of survival. Mutants, cripples, and anyone else who couldn't pull their own weight had to be killed, lest they drag the rest of the colonists down with them. The prejudice's fading is largely a result of the fact that a new wormhole was opened a couple of generations before the story and Barrayar's technology level has jumped about six centuries forward in two generations, which meant both that many disorders and handicaps could now be fixed and that there was a bit more of a safety net to catch those who couldn't perform to perfection.
This plays a large part in Karin Lowachee's books. For most of Warchild, EarthHub is at war with the alien strivs. They are seen as bestial, cannibalistic, and Always Chaotic Evil. Of course, once their society is explored, they're revealed to be a lot more complex than humans first thought. But given what the author seems to think of humanity...
Quite a bit in Warrior Cats. Although trans-Clan racism is mostly limited to stereotypes, the real racism is directed at half-Clan cats, kittypets, the Tribe of Rushing Water, and loners and rogues.
In Who Censored Roger Rabbit?, humans heavily discriminate against toons, the living cartoon characters they share their world with. Toons are treated in much the same manner African Americans were in pre-Civil Rights America, with elements such as segregated restaurants and schooling. One could even say that they were put in an "Animation Age Ghetto".
Both the Okeke and the Nuru have this toward each other in Who Fears Death. We mostly see Nuru oppression of the Okeke (according to their mutual holy book, Okeke are supposed to be slaves to the Nuru, and Okeke rebellions have a tendency to result in decades-long slaughters by the Nuru), but at least part of the oppression Onyesonwu feels from the citizens of Jwahir is that she is technically a Nuru because her father was one. Mwita's backstory involves him barely escaping an Okeke massacre of his Nuru relatives.
Discrimination against Animals (yes, the capitalization is mandatory) is an important plot point in Gregory Maguire's Wicked. Elphaba, having green skin, suffers from this too, to the point of her mother considering killing her after her birth.
In the Wild Cards series, Jokers are basically reviled and treated as second-class citizens due to their wild card-induced mutations. On the other hand, Aces, who just gained superpowers, are treated reverently by modern media, but were the subject of cultural paranoia in the past (to the point where Joseph McCarthy blacklisted Aces, not Communists). In this case, despite the presence of visible mutants and superhumans, bog-standard bigotry still exists (two of the first big-name Aces were constant victims of it).
Sometimes one form of positive fantastic racism counteracts the other though. In-story the South African Apartheid regime treated black Aces as colored, while all jokers were treated as black.
In The Witcher saga, the main character is threatened as a "freak", despite the fact that he saves people from monsters. Elves must lives in reservations, most of the people think that "good Elf is a dead Elf", and if you have an Elf in your family tree, you cannot, for example, get a wedding in a city. Other races are threatened in a similar way by humans. And in the last book, there's another group of Elves, that escaped to another dimension, murdered and enslaved its humans. And the Unicorns hate all the Elves for that.
One of local dwarf stand-ins mentioned that elves weren't that friendly themselves until humans arrived — "Oh, now when it's their turn to be kicked around it's suddenly 'we, the Old Races', right".
The elves are very good at getting their own back. For example, racist elves consider humans to be no better than rabid wolves because humans have canines and eat meat. Also, the elves despise the dwarves for having an easier time integrating in human society, and while the Scoia'tael will allow dwarves to join, most Scoia'tael leaders are elves and it is widely acknowledged in the Scoia'tael there is no way elven interests will ever be put second.
In Zoo City by Lauren Beukes there is considerable prejudice against "zoos". It doesn't help that in order to have gotten an Animal you have to have commited a violent act.
Isaac Asimov had this as a recurring theme in his works, often the form of prejudice against Earth-born humans, against robots, or both.
I, Robot has several parallels between robots and black slavery. In "Little Lost Robot", published at 1947, a scientist at US Robots, Dr. Bogert, calls repeatedly robots "Boy". In "Runaround", written at 1942, the robots stationed on Venus must call all humans "Master":
The monsters head bent slowly and the eyes fixed themselves on Powell. Then, in a harsh, squawking voice — like that of a medieval phonograph, he grated, "Yes, Master!" Powell grinned humorlessly at Donovan. "Did you get that? Those were the days of the first talking robots when it looked as if the use of robots on Earth would be banned. The makers were fighting that and they built good, healthy slave complexes into the damned machines."
In J. R. R. Tolkien's Middle-earth relations (actual contact as well as stories/myths) between various peoples are often less than rosy, both between races (Humans, Elves, and Dwarves; especially Elves VS Dwarves), but also among peoples/nations of the same race. One of the themes of The Lord of the Rings is the different races overcoming their differences in the face of a greater threat, posed by Sauron (though it should be noted Sauron himself is in control of basically a totally evil race, and so the alliance is also against them).
Note also that there's no solidarity between the "evil" creatures. Saruman's Orcs hate the Orcs of Mordor and vice versa, and within Mordor, the Orcs of Barad-dûr feud with those of Minas Morgul. It never quite degenerates into Enemy Civil War, but it works to the protagonists' advantage multiple times.
Played to a ridiculous degree in the old animated Hobbit movie. The three forces are at war, slaughtering each other, and then the orcs cross the hill and the three generals start referring to themselves as old friends...
Tolkien was deliberately vague and sparing with descriptions of the enemy. One can just as easily say the "non-white" humans are not the enemy because they are "non-white", but rather because they are allied with—or under the power of—Sauron. Also, read Sam's reaction to the dead warrior of Harad. He wonders "whether he was really evil at heart, and what lies or threats had driven him on this march so long from his home, and whether he would have rather stayed there in peace."
The Silmarillion explicitly notes that there were both good and evil factions among the "Swarthy Men", most notably when the two factions fight each other in the Battle Of Tears Unnumbered.
Also note, that J.R.R. Tolkien acknowledged the fantastic racism in LotR. He was said to have strongly regretted his depiction of the Orcs as seemingly Always Chaotic Evil and irredeemable, because it conflicted with his devout Catholicism. He often later defended the Orcs in later writings, claimed that they were simply misled and manipulated, and even said that "we were all orcs in The Great War." Just as the "evil" humans were misled and manipulated.
In The Silmarillion it's casually mentioned as an uncontested fact that it's not good for humans and elves to live mingled with one another. Good fences make good neighbours? It seems likely that this is because it would be hard on elves to see their human friends age and die, just as it would be difficult for humans to live around the eternally young and immortal. This in fact was one of the factors that led to the Numenoreans' destruction since they ended up coveting the immortality of their elf contacts. There are also practical problems as demonstrated in the original trilogy; outsiders start experiencing a skewed sense of time passing in Elvish settlements, as when the Fellowship stays in Lothlorien for about a week only to find a month has passed.
In The Hobbit the racism seems to be more from the elves part than the dwarves. Beorn shows dislike (though tolerating them) for dwarves, but that can very easily be read as him being stand-offish and not liking strangers in general rather than any disdain for dwarves in particular.