Dungeons & Dragonsplayers, as opposed to the official game universe, traditionally work out their prejudices by abusing (at least verbally) Halflings and Half-Orcs. Half-orcs are the "Dumb Brute" of the D&D game, strong, stupid, brutish, and usually unbathed. Halflings are an odd combination of every group stereotype of smaller people, including your spoiled creep of a kid brother. In an RPG, everyone can be a bully, and when they are, they generally are bullying a halfling (or a gnome). This is to say nothing of players who hate certain races for statistical or lore reasons (i.e. "Elves are always portrayed as so perfect, but they're such pushovers"; "All halflings are kender", "the rulebook says elves dislike dwarves and vice versa"), and take out those prejudices on people with favorable attitudes towards those races, in or out of game.
Though somewhat ironically, half-orcs fare significantly better among orc tribes than among humans. The human heritage grants them intelligence superior to most orcs, and they lost virtually none of the orcish natural strength for it, making them easy candidates for leadership positions.
Rangers get fantastic racism as a class feature in the first 3 editions. You select a type of monster, which could be a race, like Goblins, and get a bonus to hit and damage. Similarly, dwarves receive bonuses when attacking orcs and goblins, while gnomes get an attack bonus against kobolds and goblins; curiously, although this is explained as being due to a long history of conflict, those bonuses are one way only.
Eberron both plays this trope straight and subverts it. People of various nations are racist towards other races they've been at war with (There is also non-fantastic racism as they can be hostile to people of the same races coming from former enemy nations). Generally Goblinoids and the Warforged get the worst end of the racism. The subversion occurs in the Goblinoid Nation of Darguun. A war-torn land where the Goblinoid clans are at each other's throat, the central government barely holds everything together and slavery is both legal and regularly practiced. Despite their flaws, Goblinoids are surprisingly opened minded on the race issue, being willing to accept members of other races into their clans, should they prove worthy. Meanwhile, unlike other settings, Orcs get little racism directed at them (they don't travel abroad too much) and are also quite willing to welcome other races into their tribes (in fact, most Orc tribes often have a lot of human and half-orc members).
Warforged, Shifters, and Changelings all suffer from racism in Eberron as well. The Warforged are an artificial race of sentient constructs built as soldiers for The Last War. When the war ended, Khorvaire found itself with a sizeable population of Warforged left over - machines that think, and feel as richly as their creators, but are now without purpose. Some regard them as freaks that should never have been built, others hate them for stealing jobs (they have no need to eat or sleep), and still others would happily enslave them all again. Shifters are the diluted descendants of Eberron's lycanthropes, and many still fear them for their bestial appearance and often savage nature, as well as memories of their predecessors (who were all nearly genocided into oblivion by the local Lawful GoodCrystal Dragon Jesus religion, even the non-evil ones). Changelings can alter their appearance and gender at will, leading many to be paranoid of anyone they suspect to be a changeling-especially if they happen to actually know a changeling is in the area. Even one area of work changelings naturally excel at if they must, prostitution, has become a subject of racism and paranoia on suspicions that any given prostitute is actually a changeling-and quite possibly male in "her" native form.
Eberron also plays the non-fantastic racism. For many of its residents, race is less important than nationality is. He's an elf, whatever, so long as he's an Aundarian elf, etc...
Forgotten Realms has organizations of elves who blame their decline on either drow, humans or even all other elven subraces ("when Gold Elves ruled it was The Golden Age!). Humans in heartlands generally indifferent to most creatures with whom they aren't at war, though still wary of thieving halflings. Demihumans are banned from some places, such as Hillsfar — but then, the ruler who did it and his loyal troops aren't very popular even among humans, both inside and outside the city.
Inhabitants of Zakhara view them all as "northern barbarians". Most locals give a damn only about couples: it's okay as long as a pair of humanoids can have children; otherwise they think only in terms of natural advantages/disadvantages that matter in some professions and are irrelevant in others. For their part, the theocracy of Pantheon is mildly human-centric, but for everyone else it's just one more proof that the League deserved its bad reputation.
Many deities of differing races will often have it in their dogma to hunt, kill, capture, or just dislike other races, the elven pantheon has this in spades. The elven god Shevarash is this trope 100%, although somewhat justified given that drow are supposed to be predominantly evil.
In Ravenloft, demihumans are rare enough, and human superstition prevalent enough, that demihumans who would be tolerated in other campaign settings are objects of fear in many domains. Some domains extend this to spellcasters as well, forcing wizards to hide their powers or risk being burned alive. Even domains that don't lynch demihumans on sight usually treat them as second-class citizens. Do note that being leery of demihumans may be a rational reaction as there are an abundance of predatory monsters that look almost human in the Land of Mists.
The Vistani are Ravenloft's equivalent of Hammer-movie "gypsies", and the targets of human-on-human racism within the game, dealing mostly with the same accusations as against Real LifeRomani. Rudolph Van Richten became The Hunter because of a run-in with a particularly unsavory tribe]] and thus held a low opinion of the whole people for most of his life — until in Van Richten's Guide to the Vistani he finally had to inspect the matter in detail.
The 3E Ravenloft products introduced the race of calibans: deformed offspring of humans afflicted by evil magical influences. They're treated like menial grunt-laborers at best, and usually like Freaks In The Attic.
In Spelljammer there's a semi-secret society of humans devoted to xenophobia. Among other major groups, elves are infamous for haughtiness at best and outright racism at worst. They tend to attack goblinoids on sight, and once blew up a planet full of them. The ones aboard the eponymous ship have formed an organization dedicated to the complete genocide of all goblinoids — with no regard to whether the goblinoid in question is a child, crippled, one of the few non-evil ones, or anything else. Yes, that's right; Nazi ElvesIN SPACE!. It's kind of a weird setting.
Beholders run on a mix of this trope and It's All About Me. To any given Beholder, it's the pinnacle of all creation, the perfect reflection of the Great Mother that spawned their race. Other Beholders of the same breed are tolerable inferiors. Beholders of any other breed are disgusting abominations that must be destroyed on sight. Anything that's not a Beholder is barely worth acknowledging — little more than a fly to be swatted when it wanders too close, or a potential servant. For added fun, although the difference between Beholder breeds is sometimes quite large, other times it can be things so minuscule that nothing that's not a Beholder would even notice. The Beholder with slightly bumpier skin or a different number of teeth is as much a hated inferior as the one who has flame-based powers instead of the standard Beholder suite or has a differing number of eyestalks. Beholders in general are like this, in Spelljammer they just get an opportunity to duke it out where everyone sees it and by whole fleets.
Regular Gnomes often hold this against the Tinker Gnomes, or "Minoi", of the Dragonlance setting, because they feel their Bungling Inventor hat embarrasses all "true" gnomes. Non-minoi gnomes have even been known to form hunting parties that seek out minoi spelljammers and kill them, or at least wreck their ships so they can't spread any further through The Multiverse. Given that the minoi "spelljammers" are often ramshackle pieces of junk that are likely to fall out of the heavens and slam with devastating force into a city, and many of their other "inventions" aren't much safer, many people don't really consider this an evil act.
In Dark Sun most races are xenophobic to an extent and mistrustful of anyone other than their own kind, slavery is a way of life and cannibalism is not uncommon. The largest prejudice however is against arcane magic users and with good reason; the most common form of arcane magic is defiling. Defiling saps the life out of the users surrounds to fuel the magic, killing plants, sterilizing the soil and draining the life-energy of nearby creatures. The reason Athas is such a Crap Sack World is because of defiler magic. Another form of arcane magic exists called preserving, which is less potent but doesn't damage to the world itself. However few know the difference between the two and arcane magic users are almost universally abhorred with the exception of the Sorcerer-Kings, who are so powerful no one wants to risk angering them.
Plane Scape featured some level of fantastic racism towards the player character races, but given how many leadership positions were filled by tieflings and other such folks, it started to feel like an Informed Flaw at times. The genocidal, religious hatred between githyanki and githzerai plays it straight. However, this setting also features a genocidal, impossibly large-scale war between the Nine Hells of Baator and the Abyss, with one representing evil as tyranny and the other evil as passionate barbarism. It's Evil Romanticism Vs Evil Enlightenment acted out through genocide by races full of hate. The other immortal races also have tons of fantastic racism. Even the good ones have trouble understanding or liking each other, but at least they're "live and let live."
Dragons are always presented as viewing themselves as superior to other species, even good dragons. Some signs of their arrogance is the unconfirmed claim in 3rd edition that all other languages, except for ones spoken by species from other planes that are likely even older than the dragons, are derived from dragon language. The reason behind their ego, given in the Draconomicon, is that from the dragon's perspective, they live on for hundreds of years growing bigger, stronger and smarter, while virtually every other living thing they see grows old, gets weak, sick, and dies. Ultimately, even good dragons can't help but feel signs of superiority. How they act however, depends on if the dragon is good or evil. Chromatic dragons will consider other species to worthless and existing so that they may use they however they wish, metallic dragons look down on them more akin to viewing like children who must be helped.
Behirs and dragons hate each other. Even MENTIONING dragons around a behir Can be dangerous.
In the d20 Modern Urban Arcana setting, you have the Fraternal Order of Vigilance, a hate group bend on purging every shadow (i.e. new arrival from the D&D world) from the face of the earth.
Eclipse Phase's Fantastic Racism is mostly (with the exception of bioconservative enclaves) directed at artificial intelligences, the Artificial Human "pods" and the "clanking masses", human refugees from The Singularity who were mass-uploaded rather than being lifted into orbit, and later given cheap robot bodies so they didn't have to live in virtual reality. The nature of the setting means that many of these prejudices are just a re-sleeve away. Notably, it also explicitly mentions the Uncanny Valley as one of the issues with using a robot (or heavily modified human) body, a problem that doesn't crop up with more radical bodyplans.
Solars and Lunars are considered Anathema in the Realm, the political and military superpower of the setting, which regularly sends out groups of hunters to kill them whenever possible, and the Immaculate Philosophy. As a result, most societies teach that they're evil spirits that permanently and irrecoverably possess the unrighteous.
Sidereals are almost universally distrusted by the gods, which wouldn't be too much of a problem except all the Sidereal jobs are in heaven, and people on the ground will almost always forget any interaction with the Sidereal after a day or two. This may be as subtle as distrust or needless and unwarranted audits, or can be as direct as sending a Sidereal on suicide missions.
Terrestrials are hated by the gods, too, but they're mostly on the Fantastic Racist side of things; the entire society of the Realm is built as a voluntary eugenics program to keep the blood-line carried trait of Terrestrial Exaltation 'pure'. Mortals, especially those of weak breeding, are treated as highly expendable cannon fodder by the heads of the Realm's major houses, while Terrestrials of stronger breeding live lives of luxury on the largess of house income and a lot of slavery. On the other hand, some areas outside of the Realm, like the Varangian City-States or An-Teng, sell any child who Exalts as a Terrestrial to the Realm.
People of the Air and People of the Water are either kept as exotic shows, feared and distrusted, or slaughtered on sight. The People of the Earth have largely retreated to join the Mountain Folk, who at least let them survive, but are ultimately patronizing and controlling. The green-skinned Tree People were turned into slaves by First Age Solars, and hate pretty much everyone now. All these groups were engineered from normal human stock, under conditions where "voluntary" is very difficult to define.
Those Mountain Folk? They used to be oh-so-perfect elves, who the Solars were worried might someday act up or refuse to provide cheap labor. The Solars thus forced the Mountain Folk's creator to metaphysically enslave and castrate the entire species, almost leading to genocide. Internally, they have a massive Fantastic Caste System set up, where the beautiful Artisan class treats even enlightened members of the shorter Worker class like grunts and the Soldier class like cannon fodder.
Gods universally despise the Terrestrials, and consider humans little more than prayer sources. Celestial Gods (those of concepts) treat Terrestial Gods (those of concrete things) as backwater yokels and seldom give them their pay, and the Celestial Bureaucracy often underfunds or completely ignores them. Most gods and Exalts consider Elementals as pathetic and expendable, and the godly legal protections against summoning abuse or violation of rights are codified to not cover Elementals.
Numbers of the black-and-white spotted djala pygmies were transported in force to become pseudo-voluntary workers for the First Age Solars, bioengineered and culturally engineered them into the even smaller Minikin. When the First Age ended, almost all the minikin and djala were enslaved by Terrestrials for hundreds of years, with only small bands escaping until the Contagion let a larger group reestablish society in their ancestral homeland. In many places, like Varangia, the local society cannot hold the concept of free djala, and outside of a handful in Lookshy, the rest are slaves by sheer stubborn habit.
Beastmen are considered soulless monsters in the Realm, fit to either be hunted down or made exotic slaves. Most other countries consider them bestial freaks, insane unnatural abominations, minions of The Fair Folk, or at best an often-criminal non-citizen underclass. The few countries, like Halta, that consider them citizens do so only after a thousand years of delicate meddling by Lunars, and humans will still all leave a bar or building if a beastmen enters. They're also made the the old-fashioned way, often trained by their Lunar sires, and some tribes don't consider eating human flesh cannibalism.
The Parrot Beastmen (don'task) add an additional layer, only very recently giving up the intertribal wars, based on color of feathers, that resulted in genocide on at least three color-tribes. Now they'll just kill — often through blood sacrifice — any non-parrot they meet.
Ata-beasts and similar Talking Animals are, likewise, only considered citizens in rare places like Halta, and either enslaved or considered pets in the Realm.
Mortals with Enlightened Essence in the Realm are made monks by the Realm, or considered tainted criminals. Most places outside the Realm treat them better than normal humans, instead; in Paragon, immigrants with enlightened essence get a personal interview with thePerfect and a chance at being raised to nobility. Closer to the Wyld, though, such people are increasingly likely to be shaman that treat normal humans poorly.
Wyld Exposure can cause mutations that can be purely cosmetic, or even helpful. Because other mutations make people crazy murderers, even the least severe Wyld Mutation can result in social expulsion or death.
The masculine third gender/transgender Tya and transgender Dereth face unpleasant jokes even in their respective native culture, and Tya risk their lives if they're too visible in Coral. Outside of the West and the Delzahn respectively, or when dealing with foreigners, the cultural clashes can be dangerous or even deadly.
And, least we forget good, old-fashioned racism, there's examples like Linowan, which in addition to killing you for being a beastman or having too well-trained of an animal, will also kill or enslave you for having entirely green hair and reddish-brown skin (a common occurrence in the ''Exalted'' setting). The nearest society with entirely green hair and reddish-brown skin spy on or respond in kind to anyone that looks like they're a Linowan — or even feed them to The Fair Folk. Some racism is more subtle; the xenophobic Varangians consider foreigners simple-minded for not understanding the ridiculously complex caste system.
FATAL has a table for this. Odds are strong that you will "randomly" roll that your character agrees with the rest of his race (since making your own decisions about how your character thinks, looks and acts is anathema to FATAL). Most races hate most of the other races. Race in FATAL is determined randomly. It's like the average adventuring party is a powder keg of race hate just waiting to be set off.
Gamma World has several Cryptic Alliances that enforce this trope, like the Knights of Genetic Purity (who hate anyone who is a mutant), the Iron Society (Who hates anyone who isn't a mutant), the Zoopremacists (Who hate anyone who isn't an anthropomorphic animal) amognst others.
The elves of Magic: The Gathering's Lorwyn setting apparently have no problem whatsoever with the concept of casually hunting down and killing intelligent beings that offend their sensibilities by diverging too far from their ideal of beauty...which is, of course, an elf.
In Lorwyn's Mirror Universe, Shadowmoor, the kithkin (formerly superstitious but generally decent) become hugely xenophobic, while most everybody else is Always Chaotic Evil - except the elves, who are about the only good people around.
While not a prominent feature in New Horizon, there is an underlying current of racism that can be picked up on. The rulebook gives multiple "slang" and "degratory" titles to every race, Xanadu is explicitly stated to like Oylimpians (read: pure humans) but not other races, Medeans are sometimes referred to as the next evolution, and there is a strange insistence that Wafans are not robots, but people. Still, given that Everything Is Trying to Kill You, most of this tends to fall by the wayside.
The philosophy of the Light in Nobilis likes humanity a lot, to the point where human survival is its primary axiom, but while it doesn't specifically hate Sidhe, the clothes-people of Dionyl and so on, it doesn't really care about them - it won't go out of its way to hurt elves or balloon-people or the like, but if it came down to the survival of merrow vs. the survival of humanity, the merrow would be in serious trouble. The reverse position is held by the Dark, which mostly wants humanity to disappear, ideally by each individual human following their own self-destructive impulses to their doom.
In the old version of Old World of Darkness, racism between vampires and werewolves was built into the setting (and the various supernatural factions considered themselves superior to the "Sleepers" a.k.a. normal humans). But certain gamelines, most notably Changeling: The Dreaming, offered players ready-made prejudices and feuds between the various fairy races, under the heading "What [insert name here] group thinks of the others". The ancient immortal Sidhe, who only recently returned from Arcadia when the doors between Fairy and Earth opened again after several centuries, get it especially hard (as if being stuck in mortal human bodies wasn't bad enough). They're faery nobility, so each and every one of them must be a snobbish arrogant prick out to push the poor commoners around, go figure. Their reputation is even worse than that of the brutal Redcaps or the creepy Sluagh. Of course, it's an US American roleplaying game, so the "nobles vs commoners" stereotypes are milked for all they're worth, including a storyline clearly patterned after the American War for Independence, with the brave commoner changelings fighting the newly returned Sidhe (the British) for their political freedom.
Actually the issue between the sidhe and other fairy has less to do with nobles vs. commoners than with the fact that the commoners largely see the sidhe as having abandoned them. When banality started overtaking the world almost all the sidhe fled to Arcadia, then when the gates reopened they returned and expected to pick up where they left off.
In the New World of Darkness, things are roughly similar. Every subgroup of each of the supernaturals has a column marked "Stereotypes", giving a quick rundown of what they generally think of the others of their kind and the Main Quadology (vampire, werewolf, mage, human). The books do note, however, that it's suicide to think the others conform to that. This is doubly true for, ironically, Changeling - the new setting has "hang together or hang separately" as its theme, so whatever you think of the other seemings, you had best be willing to at least pretend to get along with them or say hello to Arcadia once again.
While schools of magic differ, a lot of the schools of magic (Mastigos particularly) consider the entirety of Werewolves to be too dumb to even use as proper slaves. Most of them treat mortals, especially those with a chance at becoming mages, as pawns at best, if they're even viewed as being worthy of attention. And a lot of potentially misguided players consider these the good guys of the new World of Darkness.
Mages in general tend to look down on the other supernatural races, but one Mage organisation, the Jnanamukti, are so extreme they freak out other mages. See, the Jnanamukti have decided that if they destroy three "corrupting elements", the Fall will be undone and Mages will reclaim the power of their glory days. Those elements? Sleeper civilisation, sleeper technology, and all supernatural races who aren't the Awakened.
Rifts uses this quite a bit. It appears chiefly with the Coalition States, who have a xenocidal policy toward D-Bees (dimensional beings) and creatures of magic, and monstrous societies such as the Splugorth of Atlantis, where humans are at best slaves, and at worst a snack.
That said, there's still racial tension among humans — at least, in areas outside of Coalition control. In the New West, Native Americans and white settlers are, for the most part, at best leery of and at worst openly hostile towards one another. The Australian Outback has a similar situation.
An important background element in the Fantasy meets Cyber Punk RPG Shadowrun, where racist tensions between humans and "metahumans" such as Orks, Dwarves, Trolls and Elves (not to mention the ghouls) are present, complete with extreme right-wing party humans advocating their persecution. Even though Shadowrun takes place Twenty Minutes into the Future of our world, normal racism has fallen by the wayside, having been mostly subsumed by the fantastic variety (as the rulebook puts it, "Why worry about the guy with dark skin when that horned thing has fists the size of your head?")
Early editions of Shadowrun had the other races refer to humans as "breeders", implying an analogy to gays (this being an actual slur used by gays towards straights).
The creators of Shadowrun have stated that the racism toward Orks, Trolls and Ghouls in the game was specifically so that typically dystopian racism could be in the game as an Aesop toward real racism.
That said, both the Japanese and Native American Nations have a degree of racism directed towards them; in both cases, this is due to the power that they've gained, as well as the shattering of the USA and Canada by Native American shamans, the rise to power of nations such as Aztlan (in Middle and South-America) and a revival of long-persecuted ethnic minorities in general, there is a backlash against "white" people in parts of the world, especially against former colonial masters.
It does go the the other way. The Japanese are arguably the most heavily bigoted group in the setting, actively persecuting any and all metahumans to a degree disturbingly similar to that of Nazi Germany (stopping just short of concentration camps), and being prejudiced against non-Japanese humans as Japan of that same time period; this goes a long way towards explaining why everybody else dislikes them.
There is one funny aversion to this bigotry: the Japanese emperor is fond of Onis, the Japanese metavariant of Orks, and has hired a lot of them to be guards around his palace and other imperial buildings, much to the displeasure of the rest of the imperial residents, who do not look as favoribly upon the Oni.
In the Elvish principalities of TÝr Tairngire (the former Oregon) and Tir na nOg (Ireland), elves look down on anyone not an elf, and non-elves are officially second-class citizens (if they have citizen rights at all). Similarly, in the dwarven enclaves and the troll kingdom Schwarzwald in the ADL (Allianz Deutscher Lńnder, former Germany) there is subtle racism against non-metatypes.
It's actually a rule. There is a 'negative' quality you can take that gives you bonus points for being prejudiced. Ironically if one is good enough at roleplaying lies to such people being racist basically becomes "free extra BP".
That said, Orks tend to get this worst. Many people are worried that their fast breeding means that they'll own replace humanity as the planet's dominant race, and their intellectual and aesthetic deficiencies don't help either. Elves and Trolls get this the least: Elves because they're pretty, Trolls because openly antagonising a 300-pound giant with super-strength and bone plating is absolutely stupid.
Transhuman Space has various forms. Biochauvinism (the belief that AIs and Ghosts aren't real people) is common, and bioroids are second-class citizens in the United States. Various combinations exist, such as the Born Human Movement, which is prejudiced against bioroids and AIs, but not Ghosts.
In Traveller the races that invented Jump drive actually call themselves Major Races. Meaning, of course, that other races are minor races.
In Traveller racism is theoretically a "not done by gentlemen" sort of thing, especially as the Imperium is based on a multicultural loyalty to The Emperor(who always ends up being human, even though adoption is a recognized means of succession). Despite that, racism is as common in Traveller as it is in Real Life.
One of the more famous quotes from Warhammer 40,000 is "Fear the alien, the mutant, the heretic." While attributed to the human Imperium, virtually every race looks down upon one another. Considering the Imperium of Man is rabidly anthropocentric, and even regularly views genetic and dogmatic deviance as punishable by death. The Eldar view every other species as lesser species to by used to their own ends, and Dark Eldar and Craftworld Eldar look down upon one anotherNote The Craftworld Eldar think the Dark Eldar are savage and parasitic hedonists, while the Dark Eldar think the Craftworlders are monkish, too self restraining, and too boring to thrive. The Orks tend to "crump any o' 'dose gits what ain't Orky enuff!" And Necrons hate the Eldar on principle due to historical racial enmity, and think everybody else is too disorderly and primitive.
Averted with the Tau, and the Tyranids. The Tau think that just about anybody can join their empire, though humans tend to be annexed as second-class citizens (depending on the world, or the source), though no Eldar or Space Marine has "lowered" themselves to join them, and the Tyranids and Orks have been deemed too aggressive and immune to negotiation to join the Tau.
"Averted" with the Tyranid species, as they are view all other species with too much mindless hunger to view any non-Tyranid with any considered racial prejudice. They are an equal-opportunity eater, and a planetary invasion often ends with them sacrificing all species on a planet, ending with themselves, into digestive pools to be used in the next generation of Tyranids.
Old fashioned inter-human bigotry also exists. The most spectacular example is probably Lastrari, which when cut off from the Imperium was taken over by the Divine Army, which instituted planet-wide purges of anyone who did not match up to their ideals. The genetically targeted diseases are positively tame compared with the 5300-mile road lined with the bodies of those who spoke out. When the Imperium regained contact, the population had been reduced from 14 billion to a mere two and a half million!
During the Great Crusade, the Imperium discovered one of the long-separated sects of mankind who called themselves the Quietude. They decided to combine human biology with technology to a degree even greater than the Adeptus Mechanicus. The Imperial fleet sent human soldiers to make contact with the Quietude and request the terms of their re-integration into the Imperium, but contact with them was lost. The Quietude responded to the main fleet by asserting that the Imperial humans were clearly genetically-engineered creatures of alien origin sent to trick them, and cited the vivisection of the missing guardsmen as evidence of this claim. As a result of this misinformation and hostility, the Imperium sent in the Space Wolves.
"Men have been denounced as mad for simply putting into practice what the Saints have preached." In principle, the Imperium would love to do this on every world it has, but most recognize that would be disastrous while they still have a wars to fight. As the Rallying cry goes...
KILL THE MUTANT! BURN THE HERETIC! PURGE THE UNCLEAN!
One of the more ostracised groups of humans are the mutants, or "Twists", humans born with horrible deformities. While they are often killed on sight on many worlds, many others are more tolerant, happy to keep them as expendable labor and second-class citizens (or third- or fourth-class, such as life is for the average citizen of the Imperium) so long as their population remains controlled tightly enough. Humans idealize the standard human form to the point that many stable human subspecies that developed after millennia in isolation are looked down upon, and many are exterminated outright.
Also, psykers (or psychics in any other setting) possess a mutation that's subtle and consistent enough to be put into their own classification aside from physical mutants. They are feared and controlled by the rest of humanity, and looked down upon as mutants and "Witches" by the orthodox humans. Unlike mutants, they do present some of the threat to humanity the Imperium propagndizes, since unchecked psykers can cause havoc by sheer power or subtle manipulations, and that's not counting the negative side effects their powers can cause...
The Gaunt's Ghosts novel Necropolis is rife with interhuman racism, particularly by the higher ups in Vervunhive, who regard the imperial guard regiments saving their asses as inferior even after displaying complete incompetence at defending themselves, they even go as far as to try and have a tank commander put on trial, in the middle of the war because he knocked down a couple of buildings due to a traffic jam the vVrvunhivers created, this quote by VPHC Tarrian towards Gaunt seconds before he gets shot really seals the deal.
Tarrian: Gak you wretched offworld scum!
On the other side, all Aliens view humans with a mixture of hatred, fear and contempt. The Imperium has destroyed thousands of Xeno civilizations over the millennia, and still strives to eliminate the survivors, with varying degrees of success.
Dark Heresy features the character talent Hatred, which gives a bonus to hit in melee combat. It can be taken for specific groups including alien races, psychic individuals, heretics, and mutants. Of note is that Hatred is available almost exclusively to the Cleric class, making it one of the biggest plusses to being religious in 40K (although it is of course required for everyone to act religious in order to stay alive). At high level, Clerics get to take the talent Litany of Hate, which lets you share your hatred bonus with your friends. In other words, hatred in Dark Heresy is a good thing (as it should be, from the perspective of the Imperium).
As mentioned, the Eldar generally have the whole Superior Species complex thing going on, but the Dark Eldar take this to a whole new level. Not only are non-Eldar species inferior to them, but other Eldar as well; they see themselves as the true scions of the Eldar race, and Craftworlders and Exodites are just weak, unworthy fools. Not only that, but Dark Eldar Trueborn (as in, members of their society who are born through the natural process rather than People Jars) also view their "Half-Born" brethren as inferior Cannon Fodder and not true Eldar. It really highlights what pretentious, elitist scum they are.
Good old fashioned Warhammer has its share of speciesism and good old fashioned racism. People from the Empire are horrifically prejudiced about Dwarfs, Elves as well as humans not from the Empire, humans from different provinces in the Empire... and of course these are the ones they'll actually talk to (maybe). Anything else will pretty much get attacked on sight. On the other hand Dwarfs consider humans to be soft and elves to be even softer as well as arrogant magic using bastards. Elves have racism within the three different factions - each hating each other to various degrees (though the worse is between the Dark and High elves) in addition to considering any other race to be little more than backwards pawns for them to use or exterminate at will.
It's arguable whether the Racism in the Warhammer games is Fantastic at all. Non-white humans in either game setting are extremely scarce.
They have Cathay for asia, Araby for the middle east, and the Land of the Dead being Egypt. Before that whole undead thing.
On the human-to-human side, Imperials and other southern human state fear and despise the Norscans due to them being frothing Chaos-worshipping barbarians intent on slaughter and conquest. The Norscans, conversely, see the Imperials and co as weaklings and sissies who worship impotent gods barely worth thinking about. Indeed, Sigmar, Ulric and Myrmidia are not even things to be hated in the unholy north, rather they are just as openly heckled and ridiculed as their worshippers. It's in fact so bad in Norsca that 'southling' is actually a fairly serious insult there.
It's just as prevalent amongst Chaos-worshipping humans in general. Norscans despise the Kurgans because they seem them as weak and so they regularly launch raids into Kurgan lands for the simple sake of butchering them (the Kurgans are nomadic, so the Norscans gain little from plundering them, and the Kurgans are about as poor as Norscans anyway). Both Kurgan and Norse are united in their distaste for the Hung, however, seeing them as treacherous and deceitful.
The Savage Worlds setting Winterweir mentions this is a constant problem in the continent of Alacarn. Humans are not prejudiced against each other by skin but they loathe people from other nations and anyone who isn't a member of their own race.
Naturally to be expected, given the attitudes of the time in Rocket Age. Add to that other racial and special tensions and things can get tense.