The Ace Attorney universe features the fictional country of Borginia. In Apollo Justice, case 3 is centred quite heavily around this country and many characters make remarks that could be considered extremely racist if said country was real. These include people stating how "lying must be a Borginian pastime" over and over again.
In Age of Wonders, it's possible to be friendly with the leaders of good and evil races, but put units from each in the same party and you may end up with deserters.
The orcs are consistently oppressed, discriminated against, and stereotyped as near-mindless subhumans. There's even a political screed in the game titled "The Orcish Problem". Half-orcs got the same treatment as orcs even though there was no difference in intelligence between them and humans. A half-orc labour organiser is one of the most eloquent NPCs in the game.
Elves and dwarves dislike each other due to differing philosophies of life and their placement on the Magic Versus Science meter (and magic and technology are actually opposed in this setting). While they're normally civil, the guards in Qintarra are very hostile towards dwarves. Elves and dwarves both dislike humans for their boundless ambition (which has caused no end of grief in the last several years), and orcs (because they're orcs), while elves treat half-elves with disdain. Nobody has a particular problem with gnomes or halflings, and half-ogres are only discriminated against in subtle ways (because pissing off someone that big is a really dumb idea).
Arc the Lad gives us the people from Holn (hometown of one of the main characters) who are distrusted by the Game's expy of Switzerland because of their ability to communicate with monsters. In Twilight of the Spirits, Human and Deimos (intelligent humanoid monsters) are locked into a cold war pretty close to heat up.
In Armageddon MUD, this trope is ubiquitous. Nobody likes elves because their culture reveres all kinds of theft and trickery, the majority of dwarves lives in slavery and are very much a disadvantaged minority because of it, half-elves are shunned by humans and elves alike, and nobody is fond of humans either, given how they hoard all the cities' wealth and high positions.
Spoofed in Atelier Annie. When Fitz is nice to Annie, but mean to her fairy master Pepe, he assumes that this trope has spontaneously manifested in a world completely devoid of it - it's actually because Fitz has a fawninggirl-crush on Annie, and is jealous that Pepe gets to spend all his time with her.
In the Bayonetta franchise, the Umbra Witches, Bayonetta herself in particular, hate the angels of Paradiso and hunt them without remorse ... however, this is justified, since the angels are in reality Eldritch Abominations that, in fact, loathe humanity as a whole and want to wipe them out along with the demons to create a world that is only Paradiso.
Her reveal trailer in Super Smash Bros. for Wii U even has her considering the Kid Icarus crew the same as the Paradiso angels from her home series, which shows off her dislike for said crew.
Hakumen refers to Kokonoe as "grimalkin",note An archaic term for a witch's cat, literally translating to modern English as "gray cat", which was used as the closest possible pre-existing English translation for bakeneko which is an offensive slang term for a beastkin, according to Jubei.
The DLC Tiny Tina's Assault on Dragon Keep for Borderlands 2 has a twistedly-meta example. Try and follow. One of the main game's PCs is Salvador. While not as diminutive as the game's many "midgets", Sal is certainly short and stumpy, and his default head sports an impressive beard. The DLC has the players (you) controlling the same characters, but now they are effectively "PCs of NPCs", because everything is a visualization of a tabletop RPG that Tiny Tina is running to entertain the PCs of Borderlands1, such as Lilith. (The "real" Borderlands 2 PCs are downstairs interrogating a prisoner.) One leg of the story has dwarves as the main enemies, and they all use a model based on Salvador's. Tina must have narrated this description to her players, although we don't hear it, because there is this exchange:
The player encounters a land inhabited by 'fiends' (monsters) who built their own civilisation after the human-fiend war. Although the first fiends you encounter are friendly towards humans since they let bygones be bygones (the war ended 400 years ago), everyone else either attacks you, sells things for exorbitant prices ('you think I'd give a human the going rate?') or expresses rather loudly that the Fiendlord should have eradicated the human race when he had the chance. There was some human racism towards the fiends in the Japanese version that was Lost in Translation — while the Fiends call themselves "Mazoku", translating along the lines of "demon tribe", the humans call them "Mamono" — this literally translates as "Demon Thing", and is a term you would usually use for a mindlessly hostile monster, rather than a sapient being.
The "Dark Ages" segregation between Earthbounds and Enlighteneds. The later ones use magic and live happy in dreams (pretty literally), whereas the former don't, and live in utter misery. That is, until the source of Zeal's power goes boom.
In the prehistoric era it's the Reptites vs. the humans, 12,000 BC features the Enlightened vs the Earthbound Ones, both 600 AD and 1000 AD have the Mystics vs humans, and the future has the obligatory Robots Kill All Humans philosophy.
City of Heroes has two primary alien races. There's the Rikti, most of which want to kill every human on the planet. Then there's the Kheldians, half of which are good, half of which are evil. There's many people, players and NPCs, who believe all Kheldians are evil, and believe the policy should be to shoot first and ask questions later. The Rikti also have a few "good" ones. They've been tricked by Nemesis into the war they're waging on humanity, and most of the ones who are still fighting are the ones who don't know this or don't believe it.
Command & Conquer: Tiberian Sun: There is quite a lot of hostility between the mutant and human factions, who deride each other as "blunts" and "shiners" respectively. Nod in particular regards the mutants as abominations and sees no problem with slaughtering them for their own ends; GDI meanwhile pretends to help them and call them allies which however is purely for hollow PR measures.
While Undead in Dark Souls run a danger of becoming mindless, violent hollows should they lose all of their humanity, Undead that still have their sanity intact are still treated as abominations and horrors by the people of their world. About the kindest treatment an Undead can expect is being locked up in an isolated Asylum where they are left to rot until the end of the world comes, unable to die even if they wanted to. It's no wonder so many of them flock to Lordran based on a shaky, very sparse prophecy about "the fate of the Undead"... it's the only hope they have left in the world.
The Deus Ex series has this, most notably in the newer entries.
Deus Ex: Human Revolution has this with tension between augmented people and non-augmented people. The latter dislikes the former for a multitude of reasons, such as religious objections to playing God, how augmentations could create an economic divide between those that can afford it and those that cannot (i.e. why hire 5 naturals when you can hire 1 augmented person?) and the concerns with the drugs needed to use it.
Deus Ex: Mankind Divided has this coming to a head in the aftermath of the aug incident at the end of HR that caused augmented individuals to violently attack people indiscriminately, resulting in ghettos for augmented people, where they are treated as less-than-human.
Deus Ex: While barely seen in game, probably since the hubbub about augmentation is now decades old, supplemental materials such as the Deus Ex Bible and a promotional copy of one of the in-game newspapers show that augmented citizens are viewed with disgust and suspicion. To add to the fire, the new wave of nano-augs, which the player is a member of, receive tension from the mech-augs, since they can "pass" in society, whereas mech-augs cannot.
In the Diablo universe, humans are descended from the Nephalem, who were born from the union of angels and demons who were tired of fighting the Eternal Conflict and created the world of Sanctuary, which humans now call home. Many demons prefer to expunge humanity to the last — Belial tells you that Azmodan will "exterminate you and every last one of your misbegotten kind" when you reveal him for who he really is, and Azmodan himself calls you and humanity in general "creation's greatest sin." The angels aren't that much different — while a number of angels aren't fond of humanity (Imperius in particular would rather purge Sanctuary because "demons had a hand in making it exist"), some are, with Tyrael, Itherael and Auriel voting to spare Sanctuary from annihilation. Imperius was flat-out against; Malthael abstained (mainly because he was absent from the council due to Worldstone-related matters when the vote was made), but it was counted against. Zoltun Kulle, twisted though he may be, even lampshades this.
Zoltun Kulle: Angels are no better than demons. Did you know that they once voted on whether or not to eliminate all of mankind? Only one vote spared us from extinction. Player: Tyrael. It had to be Tyrael. Zoltun Kulle: Yes. Whatever else he may be, he is the aspect of Justice... and there is no justice in murder.
Despite the game's humorous, light-hearted nature, one of the central underlying themes of Disgaea (mostly the first game) is racism, particularly the issue of judging a group without actually knowing them. Lamington talks about this before the final battle. Almaz says something similar in the third game, even admitting his own pre-game prejudices.
A lot of the villains in Dissidia: Final Fantasy have a habit of referring to Zidane & Kuja with terms like "simian," "monkey," etc.
Dota 2 has Tresdin the Legion Commander. This hero formerly used the model of Grand Marshall Garithos (see below), so his racist lines were used. When she was introduced in the game, the racism remains as she is a pro-human supremacist, but the racism can get into hilarity as she will use the line "Never trust an X" in nearly ANY species she came across (like trees)... AND several other jobs she finds disgusting (like sorcerers), as well as getting confused on some indistinguishable species (like Faceless Void), prompting a confused "Never trust a—What are you anyway?" The one species that looks like she hates the most? BEARS
Dragon Age: Origins is full of this. Elvish racism against humans or elves who act "too human". Human racism against elves, which is much more pronounced than the former. Human racism against humans of other ethnicities and nationalities. Classism in the Dwarven caste system. Prejudice and mistrust against Circle mages. Executions of non-Circle mages. Religious intolerance, schisms and Holy Wars. There's probably not a permutation of this they don't cover.
Humans and Dwarves. They are pretty respectful of each other for the most part, although the Dwarves view living on the surface as a weakness while human think the Dwarven caste system and politics are ridiculous. But there's no hostility.
Dragon Age II adds Qunari to the mix. It's mostly a religious conflict, but the anti-Qunari zealots don't hesitate to throw around terms like "ox-men" when referring to the Qunari. For the Qunari themselves, those who follow the Qun are people, and those who do not are things.
Mages are a trickier situation as many people point out that there are many legitimate reasons to fear mages and want some sort governing power over people who can accidentally summon a demon and a zombie army big enough to wipe out a village. If that wasn't enough, DA II gives plenty of examples. Sure, sometimes it is bigotry. Sometimes, it is a very understandable concern about people with destructive power that also happen to constantly hear voices of demons.
Though the aforementioned Qunari seem to view mages as unthinking monsters and treat them as such (their word for them; "Saarebas" literally means "dangerous thing") by sewing shut their mouths and eyes and keeping them in painful looking shackles at all times. Their hatred of mages is such that during a particular encounter, if Hawke mentions they or one of their companions use magic, the Qunari will immediately attack even if a peaceful resolution had made itself apparent.
In Drakengard3, Mikhail hates Wyverns, seeing them as nothing but pathetic Dragon-wannabes and enjoys slaughtering them whenever he encounters them. It's particularly jarring since Mikhail is otherwise the sweetest and nicest character in the entire series.
The player-base often (jokingly) demonstrates a huge amount of hatred and disgust for the Elves, often going so far as to treat them as the mortal enemies of the Dwarves. Most of this is due to how the Elves subtly insult the Dwarves when trading, try to instate limits to how many trees the Dwarves can cut down for wood, bring crappy trade goods, refuse to buy anything made of wood (even though they themselves sell items made from wood), and if they siege the player, they attack in their thousands and wear crappy armor that the Dwarves can't wear or smelt down into metal bars. This isn't helped by the Elves eating their enemies, and like to start wars over the treatment of plants (then eating whoever they fight); they basically are designed to be as unreasonable as possible, whether or not they're at war with you.
This is especially funny given the existence of a race that already behave as the Dwarves' mortal enemies, the Goblins.
The player base takes this further, discussing the best way to commit genocide against Mermaids for their bones. This, despite their bones only being useful for improving trading and fortress reputation, so horrified the creator that he nerfed their value to nip it in the bud.
Humans in Eien no Aselia tend to look down on spirits to a great extent. The spirits themselves seem to take it for granted by this point until Yuuto starts making a fuss.
In the background lore, the Bretons and Orcs hate each other, the Nords and Dark Elves hate each other due to war, the Argonians and Dark Elves loathe each other due to slave raids and slavery by the latter, and the Khajiit and Wood Elves regard each other with hatred, both of them raiding each other's homeland. The High Elves and Dark Elves, in particular, are both racist against all other races.
Even if you play a Dunmer in Morrowind, you're still considered an outlander. It's not a question of race so much as culture. And the Ashlanders consider all other Dunmer as outlanders. The absolute worst insult in Dunmer culture is "N'wah", which means "foreigner".
This gets even worse in Oblivion when you hear rumours of a countess interested in species 'purity' and torturing Argonians, then find a torture chamber in their castle.
In the Shivering Isles expansion, one NPC is terrified of cats, and he has a pet dog. And he has the unfortunate problem of a Khajiit that happens to really like his dog, resulting in him being constantly wary. If you are a Khajiit yourself, you can't even take his sidequest, and he'll sic his dog on you!
In the first game there were Jesters that would make offensive jokes about your race.
Valen Dreth, the first NPC you meet in Oblivion, has a nice rant to deliver against whichever race you may be, even if you're a Dunmer like him.
Many of the Stormcloaks have this attitude, especially in their capital of Windhelm, where the Dunmer are forced to live in a slum and the Argonians are only allowed to live and work on the docks. According to Brunwulf Free-Winter, one of the few Nords trying to make things better for the downtrodden in the city, Ulfric will not even lift a finger to help non-Nords in his hold of Eastmarch.
The Forsworn, the native Bretons of the Reach, despise the Nords and the Stormcloaks in particular for their actions against them in Markarth. The fact that they resort to murdering people in the city and consort with Hagravens keeps them from being too sympathetic, but it's worth noting that many of their arguments make a disturbing amount of sense (particularly about how they're not allowed to worship their own gods, which any Talos worshipper can relate to).
Khajiit are banned from cities due to the belief that they're all murderous skooma-addicted thieves, and Argonians are mostly only allowed to work at docks. There are also racial slurs that are unique to both, like "lizards" or "boots" with Argonians and "cats", "rugs", and "carpets" with Khajiit.
Dragons despise mortals, though this is much harder to catch as most dragons speak in their own language. However almost all of this dialogue and when it is you find a lot of hate toward non dragons. Dragons who don't wantonly slaughter mortals are incredibly rare.
In Fallout 2, Vault City residents hold themselves superior to all others, having achieved instant success at society-building from the moment they left their Vault. Their leader, First Citizen Lynette, has strong prejudices bordering on genocidal, against ghouls, mutants, savages and anyone living above-ground when the bombs landed.
General hatred of Super Mutants is widespread, given that only a few decades prior the Super Mutants had every intention of overrunning, destroying or mutating all life. Several mutants, including the one you can recruit, seem to still hold mutant elitist philosophy as well.
In Fallout 3 if you allow Fawkes (one of the two friendly Super Mutants in the whole game) to become your ally, he comments that people may hate him, but because of the player's reputation they'll never say anything.
Ghouls are people who have been hideously mutated by prolonged exposure to radiation. There are feral ghouls which can't be reasoned with and attacks anything on sight, and there are civilized ghouls, which are pretty much just friendly NPCs without skin. Naturally, the population of the wasteland tend to mix this up and treat all ghouls as monsters. This conflict is vital to the quests "You gotta shoot 'em in the head" and "Tenpenny Tower."
A subversion in Fallout Tactics: Brotherhood of Steel- having to recruit tribals from outlying settlements goes against their own ideals just on its own, but the epynomous organization also accepts ghouls and intelligent deathclaws into their ranks despite the objections from Simon Barnaky. After he is captured and Dekker takes command, super mutants and reavers are also allowed to join.
In Fallout 4, the people of Massachusetts are constantly holding Witch Hunts for "synths", Ridiculously Human Robots created by the secretive and malevolent "Institute" to infiltrate wasteland society for nefarious purposes. This would be all fine and dandy if it weren't for the fact that many synths are sentient, and a good number of them hate the Institute as much as everyone else. The Brotherhood of Steel in particular are very anti-mutant as well as anti-Synth. They don't even make an exception for one of their own loyal members when he's outed as a Synth.
In Final Fantasy VI, the Espers are the Other race that is being literally used by the humans. Terra's existence as a 'mixed' lineage child and the problems she has because of this are obviously her working through the 'racism.' The empire treats Espers as basically magic batteries, not even acknowledging them as living creatures, and they're the only ones who are interacting with espers right now. Even the Returners talk about Terra in terms of her power and usefulness in their fight. Sometimes they don't even talk to her about it even though she's right there.
The town of Thamasa, founded by the last Magi after they were hunted down and killed following the war. When the party goes there, the townspeople refuse to let them use the shops because of their continuing mistrust of outsiders, although that changes after the party helps rescue Relm from a house fire.
In Final Fantasy VII, after he goes insane, Sephiroth first believes that the humans betrayed "his" species, the Cetra, and develops a hostility bordering on vendetta towards them. After he finds out the truth (that what he was "cloned" from was not one of the Cetra, but something quite different), he just becomes completely evil without any particular prejudice.
In Final Fantasy IX, the Burmecians are referred to as 'rats' and 'rodents' as a racial slur by those attempting their genocide.
Friendly NPCs are often shown to be afraid of Vivi because he's a black mage, and most of their experience with black mages involves them destroying their cities.
Nobody even once raises an eyebrow or disrespects any members of the Qu race, despite them being universally depicted as food-obsessed, bumbling, baby-talking clown-looking things. Though this may be due to their obsession with food making them great food critics and chefs.
In Final Fantasy X, the stateless Al Bhed tend to be looked down on by regular humans, with the Church of Yevon being particularly harsh due to the Al Bhed violating Yevon's restrictions on the use of technology. Even Wakka is shown throughout the game to be distrustful of Al Bhed, though he becomes less so the further along the story gets. For this reason, they use goggles to hide their distinctive eyes when outside their home. In the sequel, with the Church of Yevon severely weakened (when it's your god's fault everything was crap for so long, it's hard to keep worshipers) and machina usage slowly growing, the Al Bhed are slightly more welcomed... but one of the themes of the game is how hard it is to shake old beliefs.
Used to hell and back in Final Fantasy XI. Beastmen hate the player races, the player races hate Beastmen, Humes exploit African-AmericansNative-Americans Galka, Elvaan are snooty to everyone, and even the cutesy Tarutaru have performed genocide on walking, talking frogs. To top it all off, the Precursors hate everyone but them. If there's a solid theme to FFXI, it's Fantastic Racism.
The beliefs held by the inhabitants of Gran Pulse seem to be a mirror of this. To them, however, Cocoon is interpreted as more of a false utopia.
In Final Fantasy Tactics Advance, the main character Marche unknowingly refers to a bangaa (a race of reptilian humanoids) as a "lizard", which is soon revealed to be a form of ethnic slur against them. Though this is probably similar, if not equivalent, to someone calling you an 'ape' (Something that happens a few times to Humans in fiction, too) The lizard comment is used by some NPCs in Final Fantasy XII, and there are other indications of fantastic racism in that title, the most notable being a comment that "The Emperor is willing to overlook race for his more talented servants."
Final Fantasy XIV has some racial tension between the playable races, though it's very subtle and the majority of the characters get along for the most part. The beastmen, however, are hated by everyone due to said beastmen trying to capture people to be used as slaves that empower the primals for each beastmen tribe and using said primals to destroy and take over Eorzea. At first, the Slyph are the only beast tribe that are actually friendly with its neighbors and don't wish to cause any harm. As you progress in the main story, you get to see members of other beast tribes who are not hostile and are willing to work with other races to strengthen the relationship between the two sides (though the friendly beastmen are very small in number compared to their hostile brethren).
In Binding Blade and its prequel, Blazing Sword, the nomadic people of Sacae are disparaged by the "civilized" countries of the continent. In Blade, Bern carries out an ethnically-motivated slaughter of the Sacaeans and one recruitable character is dead-set on revenge when he escaped thanks to looking more like someone from Bern due to his Mixed Ancestry. In Sword, there is Marquess Araphen's hatred for the nomadic people of Sacae, which includes our plucky heroine and his very own captain of the guard. After the Marquess snubbed Lyndis, that captain of the guard promptly told Araphen to shove it (Araphen trying to tell him he was one of the "good ones" just made it worse), looted his treasury, and stormed off to join Lyndis.
Fire Emblem Fates has the dueling nations of Hoshido and Nohr. Interestingly, although the game portrays Hoshido as "good" and Nohr as "evil", all the racism is from Hoshido against Nohr. "Nohrian scum" is practically Hinoka's catchphrase, and variants on it are used by every Hoshido character not named Corrin. Although Nohr is the aggressor in their warfare, nobody from Nohr says anything similar about Hoshido (with the exceptions of characters we aren't supposed to like). This rather jaw-dropping display (the heroic country is astonishingly racist while the villainous country is rather egalitarian) is a large part of why the game can't be deemed Black and White Morality.
In the FreeSpace series there is constant tension between the Terrans and Vasudans, with Terrans seeing Vasudans as superstitious, smug assholes, Vasudans seeing Terrans as idiotic, violent brutes, and constant bickering and racist comments between Terran and Vasudan characters. The slur "Zod" used by Terrans to refer to Vasudans has appeared so often in fan works that it has become Fanon. At one point in the second game, the player character serves on a Vasudan ship as part of an officer exchange program to soften the racism.
FTL: Faster Than Light: In a galaxy where humans coexist with many different kinds of aliens, such as the Ambiguous Robot Engi and the Energy Being Zoltans, as part of The Federation, the Rebels are out to crush the Federation, especially non-human entities. This is reflected in-game—all Rebel non-automated ships that haven't been hijacked by pirates, including the Rebel Flagship, use crews composed strictly of humans.
Racism plays a pretty large role in a lot of the events involving multiple races (beginning with humans-versus-Zombies, humans-versus-Aliens, humans-versus-vampires... see any trends?), especially Halloween 2008's "humans-versus-vampires-versus-elves-versus-zombies" free-for-all (due to a misinterpreted prophecy).
The possibility that Gaia's orcs have been enslaved is brought up.
In Lunar: Dragon Song, the humans, beastmen and the Vile Tribe hate each other. Eventually the beastmen learn to accept humans, and the Vile Tribe generally accept anyone who forsakes Althena and own darkness in the form of crystals as their own (near the end a few begin to question themselves).
Vile Tribe versus humans also comes up in Silver Star Story. Eternal Blue might be the only game in the series that doesn't have some Fantastic Racism against the Vile Tribe (if you don't count the Childhood's End tie-in manga).
Shaper-to-creation racism in Geneforge parallels institutionalized slavery in America, down to the belief that creations who run away are mentally ill. At their worst, Shapers can't even conceive of the idea that creations might have rights, any more than you'd conceive of granting rights to a hammer or a saw. "Rogue" creations, for their part, view Shapers as a blight to be annihilated, and don't always distinguish between actual Shapers and normal humans. Meanwhile, drayks (incredibly powerful creations that the Shapers regret making and kill on sight) look down upon other creations as inferior, and are in turn looked down upon by drakons (drayks that learned how to rewrite their own genetic code for increased power). There's also a divide between Shapers and normal humans, but this can work out multiple ways—some people hate and fear Shapers (though not too openly), some venerate them, and some just accept them as a part of life.
In The Lost Age, the werewolves of Garoh, precursors/descendents (it's complicated) to Dark Dawn's beastfolk, were persecuted for transforming into wolf-people under the full moon (not helped by their inability to speak while beast-like).
In the history of Weyard as described by NPCs and encyclopedia entries in Dark Dawn, it quickly becomes obvious that the "Golden Age of Man" was only golden if you were one of the Smug Super overlords. Among other things, the racial name of the non-powered people was used as a slur, and beastman slaves were used to build Apollo Sanctum. This latter one is in fact a major plot point, since it means that the only known set of safety gear for use in said dangerous building is made for beastfolk and won't fit anybody else.
Guild Wars did not delve into this extensively until the Eye of the North and its sequel gave non-human races a significant role in the story. The Stone Summit are dwarves who believe all other races are only worthy of being slaves. The Centaur and Tengu are deeply resentful of other races, particularly humans, for infringing on their territory and humans often treat them as little more than beasts. The Ministry of Purity espoused the extermination or exile of all non-humans, and the Emperors have adopted that belief. Charr and humans have a deep-seated hatred for one another reaching back centuries due to their constant wars for control of Ascalon. Asurans in general classify skrit as vermin that should be exterminated while the Inquest views all other races as fit only for labor.
Gungnir has a lot between the Leonicans and the Daltans. The entire reason the game starts is due to the Daltans being extremely oppressive to the Leonicans.
The various species of the Covenant are shown to mostly dislike each other. The Elites see themselves as superior to all other races apart from the Prophets, with particular (and mutual) hatred for the Brutes. The Hunters respect only the Elites, and see absolutely no moral problem with arbitrarily killing lesser Covenant species. The Drones resent the superior technical expertise of the Engineers. The Grunts are oppressed and bullied by everyone else, particularly the Jackals, who themselves resent their low position in the Covenant pecking order. The Prophets generally prefer the Elites, until they switched their favor to the Brutes and ordered the genocide of all Elites.
The entire reason why the Covenant are attempting to destroy humanity because they believe the very existence of humans is an offense to their gods. After the war, there's a still a lot of hate lingering on both sides; some Covenant remnants still want to finish the job against humanity, and a number of human supremacists refuse to even consider the idea of allying with human-friendly aliens (even though the only reason humanity survived the war to begin with was because they were able to ally with Covenant defectors).
The Forerunners followed a religious creed known as the Mantle, which teaches that the Precursors told them they should protect and lead all other life. Unfortunately, for most of them this translates to "Our gods told us we're better than everyone else". Their children are taught that humans are no better than animals, some of their scientists revere humanity only as objects or constructs, and the most powerful leader in their government seems to use their equivalent of the n-word towards other species in casual conversation. The racism also extends to different castes ("rates") in their society.
While not in-game, multiplayer suffered quite a bit of anti-Elite speciesism. This may have something to do with "They're harder to headshot from behind" regarding SWAT, but the slur "Dinosaur" seems to come up too many times for it to be just that. Seriously, try making a thread on the forum about those guys, and you will invariably get at least one comment about "they're dinosaurs" and about -5 posts about how they're fun to play as. Say anything about liking to play as them, and you'll get called out on it because of the aforementioned headshot problem.
Hatoful Boyfriend has it mixed in with classism and ableism in the views of noblebird Shirogane Le Bel Sakuya. He sees his half-brother, who had a common-born father, as a "mongrel"; he calls the less intelligent Okosan a throwback; he has racist terminology for a dove from the Philippines, and if he likes the Token Human protagonist he can once tell her "You are a credit to your simian ancestry." BBL and supplementary material show that humans and birds fought a war once that lasted three decades and left humanity a tiny shadow of itself, living in caves and sometimes indulging in guerilla warfare or terrorism, and so many birds want to finish the job of wiping them out. Holiday Star has a scene where the protagonist is discouraged from visiting a high class department store because she's human.
This drives the whole plot of the online trading card game "Hex: Shards of Fate". The Ardent and Underworld alliances both fight against each other, but each race within the factions has a particular hatred within the other faction. The humans started a war with the necrotic for using hexing gems to defile their sacred tombs and reanimate the corpses of their dead kings and loved ones. The nature-loving elves vehemently oppose the dwarves, who believe that their sole purpose is to use their war machines to spread destruction for the sake of destruction. Some of them are even trying to dig out so much of the underground that the entire surface world will collapse. The Shin'hare (rabbit warriors whose society is based on feudal Japan) want to conquer the whole world starting with the Coyotle (peaceful plain-dwelling coyote people who society is based on Native America) because they want to steal coyotle secrets to controlling the weather. By far the worst conflict is the one between the Orcs and the Vennen (cave dwelling spider people). They both want to wipe each other out rather than simply enslave their enemies. The Orcs use non-lethal traps against all sorts of other races so they can be put into the arena for gladiatorial combat. All except the Vennen, because they consider it an honor to feed their mountain god with either your blood or the blood of your opponent and anyone who enters the arena is given at least a little bit of respect. The vennen are an all-male race that reproduce by capturing orcs and using the as incubation slaves. The human alliance was a reluctant one because both the Orcs and the Vennen are aggressive and sadistic but the Vennen torture their prey while the Orcs at least give their opponents a chance to fight back.
In Jazz Jackrabbit Devan Shell decides to invade Carrotus...because he read "The Tortoise and The Hare" and came to the conclusion that the lesson was "All lagomorphs are smug, superior jackasses," and decided to show them a thing or two by eradicating them.
The Vektans of Killzone view the Helghast as fascistic mutants while the Helghast view the Vektans (and by extension, the United Colonial Army) as evil oppressors. They're both right.
Kingdom Hearts II gives us this little gem from DiZ: "A Nobody doesn't have a right to know. Nor even does it have the right to be." The only Nobodies he had met before had thoroughly screwed him over and destroyed his entire world back when they were human, so he has a right to be bitter. He did apologize to Roxas after learning he was capable of feeling emotion.
On Taris, the only nonhumans who can walk around in the Upper City work for the local Exchange boss or are pretty Twi'lek shopkeepers. Others get pelted by stones thrown by children, as seen once. There is a street preacher calling nonhumans a "plague that sweeps through our streets". A seedy hotel has alien occupants despite this being illegal. The slum-like and generally miserable Lower City, overrun by gangs, is where most of the nonhumans live. The racism Juhani experienced as a child on Taris is a major point in her sidequest.
In the second game, both Atton and Kreia have strong prejudice against droids. Atton describes droids "break in the head". Kreia also hates certain types of aliens such as Zabraks. It's likely that these attitudes are a result of the fact that she can't read the minds of aliens and droids, making their actions harder for her to predict and control.
In Star Wars: The Old Republic, the Sith Empire is largely bigoted towards all species who are neither human or Sith Purebloods. Playing an alien Imperial will net you a bit of hostility from quite a few people. However, there are more than a few alien Sith Lords who have proven themselves and by the time of the Hutt Cartel, the Empire is in such dire straits that they're not in a position to turn away potentially useful assets.
Legacy of Kain has a three way racial conflict. The Ancient vampires and the Hylden were two Precursor races who considered themselves godlike. The Ancients began a holy war against the Hylden because the Hylden would not submit to their god. Hylden were banished to a hell dimension, but cursed the Ancients with blood thirst in revenge. Humans began to hate vampires, seeing them as a pestilence. As the vampire population became more turned humans than originals, they began to see themselves as dark gods, superior to humans and rightfully deserving to rule the humans. The Hylden, meanwhile, had a bitter hatred for vampires for their banishment, extending to vampires turned from humans who were so far removed from the original vampires that they didn't even know the ancient history. The Hylden also looked down on humans as inferior beings, but for the most part, the humans are unaware of the Hylden's existance.
The Legend of Zelda tends to be a very bizarre case. Hylians, who form the general "human" population of Hyrule, are said to be the chosen race of the gods. This actually *does* place them on a superior level to all other races in the kingdom, and only the Gerudo seem all that bothered by it. One of the lamentations of the Downfall Timeline leading to the classic games is that, due both to interracial breeding and a war after The Legend of Zelda: Ocarina of Time, purebloods of the "chosen race" are nearly extinct.
In The Legend of Zelda: Majora's Mask, certain shop owners refuse to do business with a species other than their own. This is mainly geared towards Deku Scrubs, although the shop owners may simply have qualms about selling dangerous items (such as bombs) to children. The guards at every exit of Clock Town refuse to let Link's Deku form by, because it would be dangerous for a child to leave town. Similarly, the lady running the Treasure Chest Shop charges thirty Rupees for Goron Link but only five for Zora Link, though a higher entry fees result in better rewards.
Mass Effect has this against and/or between every sapient species shown in the trilogy. Your actions throughout the games can improve interspecies relations somewhat, or actively make them worse.
Krogan are viewed by pretty much everyone in the galaxy as mindlessly violent brutes who only want fighting and killing, a reputation the krogan aren't interested in dispelling (especially as most krogan who leave their homeworld do so to join mercenary gangs). Krogan themselves absolutely hate the salarians and turians due to making and deploying (respectively) the Depopulation Bomb 1000 years ago that's turned them into a Dying Race.
Humans aren't exactly liked by the wider galactic community for their rapid and aggressive expansion, having a disproportionately powerful influence on Council space and viewed as bullying newcomers muscling their way into systems made by the more established species. The batarians hate humans especially, blaming humans for the loss of potential colony worlds they had claimed and performing a lot of slavery raids and terrorism against human settlements in retaliation. Meanwhile there is a lot of bad blood between humans and turians specifically, given that turians performed First Contact by blowing up human ships and conquering one of their colonies, and humans are understandably miffed towards the batarians for aforementioned slaving and terrorism. Particular humans formed Cerberus, a terrorist organisation dedicated to galactic human dominance, and Terra Firma, a political party which advocates human isolation and nationalism.
Everyone ostracises the quarians for creating the geth, blaming them for the Robot War that only affected their race and left the quarians without a homeworld, with most planets actively refusing to even let their Migrant Fleet enter their space and widely regarded as nothing but beggars and thieves. The writers did their research in relation to real life oppression of traveler peoples, showing that widespread discrimination makes it difficult for quarians to get legitimate work, causing many of them to turn to beggary and thievery to survive outside the fleet, and the Codex notes that many of the companies that petition governments to ban quarian workers are the same ones that make backroom deals with them to exploit their skills while paying them much lower wages than they would normally.
The rachni, despite being extinct for 2000 years, are feared and hated universally due to an ancient war against the rest of the galaxy. Wiping out the last rachni on Noveria gets only token objections from your squad (who don't even advocate for her specifically, just that genocide is wrong), and the turian Councillor's admonitions are more because he hates you and everything you do; if you save the rachni he's utterly convinced that this will mean the end of the galaxy in a few generations.
A clever inversion of expected prejudices happens with asari mating. The all-female asari species can reproduce with any other species. If you discuss this with your asari teammate, she'll explain that union between two asari is looked down upon as nothing has been gained. Indeed, she herself suffers under the stigma of being a "pureblood."
The second game adds some justification to this prejudice, as apparently the Ardat-Yakshi (asari who inflict Death by Sex) are dramatically more likely to be born from a union of with a pureblood, so societal prejudice against these kinds of unions is in many ways an overt attempt to stop these creatures from being born (unfortunately, about one of every 100 asari is to some degree an Ardat-Yakshi). In the third game one of the monasteries where Ardat-Yakshi are housed away from society are seen, and Liara, an asari, talks about the Ardat-Yakshi in what would be a very dehumanizing way if they weren't, well, asari. The asari believe the condition prevents sufferers from developing empathy, but most Ardat-Yakshi are not actually monstrous - those who are are just very high profile. Then again, some squad mates point out that other races might have simply killed their equivalents to Ardat-Yakshi.
Ashley shows what looks like outward hints of fantastic racism by not trusting the alien team members at first, though a lot of her concerns are justified by her being in charge of operational security on the Normandy, and the alien crewmembers include a turian (whose species have had a violent history with humanity), a self-admitted quarian drifter, the asari daughter of the Big Bad's second in command, and a krogan mercenary - pretty much the most untrustworthy thing in the galaxy. Her issues stem from her belief that the other races will abandon Earth when it needs help. She also strongly dislikes Terra Firma and Cerberus for being too hostile towards alien races. By Mass Effect 3, her mistrust of aliens is gone and she's able to work well with them.
AIs suffer extensively more so than even the quarians. Roughly half of the AIs one encounters in the game have justified reasons for being misguided antagonists, and the other half aren't even antagonists - their inability to communicate means they can't even protest when people kill them. The best they can do is self-defense which, naturally to many in the setting, looks like an AI gone rogue.
Geth specifically are viewed as a dangerous threat, due to first completely shutting themselves off from the rest of the galaxy, any ship sent to make contact with them destroyed, and then a splinter faction joining the Reapers. At the time the game takes place, most of the geth would like to make peace with the rest of the galaxy. But the prejudice against them is only half of the problem: they don't really understand organics either, and they know they need to be cautious until they can find some common ground. The prejudice against the geth is so severe that if you wipe them out in the third game, only EDI (herself a synthetic), Tali and Liara are not fully pleased with it.
Perhaps the most hated race are the vorcha. No matter where you are, most races view them as nothing more than vermin. This attitude is not helped by the position that evolution has left the vorcha in. A lifespan of twenty years means very little opportunity to become educated or integrate into society or even form a society of their own; they're only spread around by stowing away on ships visiting their homeworld.
Batarians were implied to be the Token Evil Teammate of the Council races, having a totalitarian government and practicing slavery as part of their culture. Then their anger at human expansion caused them to sever ties with the Council and become a rogue state, getting heavily into criminal and terrorist organisations, being viewed as the pinnacle of societal evil in the galaxy much like how the krogan are viewed as the pinnacle of personal evil.
Sovereign/Nazara sees all organic life as a mistake that its brethren need to periodically correct. This contradicts the motive of the Reapers as revealed in the third game, but originally their motives were quite different than in the final product.
Mass Effect 3 introduces Javik, a Prothean who's been in stasis for 50,000 years. His bigotry towards the "Primitives" of this Cycle is a prevalent aspect of his character, often coming across as dismissive of various races, bemoaning their lack of potential from what the Protheans had expected from them and occasionally indulges in light-hearted mockery. He seems to genuinely loathe salarians, though. He's shocked at the possibility that the "lizards" could achieve sapience and frequently expresses disgust or contempt for them and their evolutionary past.
Saren in Mass Effect hates humans more intensely than probably anyone else in the galaxy, up to and including sabotaging then-Lieutenant Anderson's attempt at qualifying as a Spectre. According to the novel Mass Effect: Revelation, his Freudian Excuse is that his brother was killed in the First Contact War. This makes all the more notable that, by the end, he comes to view Shepard as a Worthy Opponent.
Within Turian society, Biotics are ostracized and mistrusted due to their relative rarity within their race (the trilogy having only two named Turian Biotics) and as such tend to end up becoming mercenaries rather than continue service in the army.
The Leviathans consider themselves the apex race of the galaxy. All other races are nothing more than potential slaves to them.
Kai Leng, in the books, considers asari physically repulsive and is itching for a reason to teach any alien a lesson in human superiority (though this trait is much less pronounced in his in-game appearance since you never really meaningfully interact with him). Similarly, Maya Brooks and the Shepard Clone of the Citadel DLC in the third game considers Shepard to be a race traitor due to them actively trying to save the galaxy at large rather than simply letting the other races get murdered by the Reapers.
Regardless of morality, Shepard says that an AI is "not even alive, not really" and is "just a machine, and machines can be broken". Fortunately Paragon Shepard learns understanding after meeting Legion. Renegade Shepard on the other hand hates every single non-human species in the galaxy; on top of endorsing all of the above and frequently disparaging other species on their inferiority to humans, they deliberately kill off the Council so humanity could seize control, willingly and enthusiastically support Cerberus, commits or enables genocide against at least three different species, and calls a hanar a "big stupid jellyfish".
The universal racial/species insult is to address an individual by the name of their species, especially so if one already knows the name of who they're talking to. This applies across the board.
In Neverend, the humans despise the Auren, a race of fallen fairies. The supposed reason for this is the Auren siding with Sorcerous Overlord Enakhaan in the war for the kingdom many years ago. The heroine, Agavaen, is called "Auren witch" several times. Her sister Denevera speaks of how discrimination against the Auren has turned her against humans.
Another Bioware game, Neverwinter Nights, also pulls on this, more so in the first game than the second. In the first game, talking to common people on the streets would garner variable responses depending on your race or even class. The only race not discriminated was (surprise surprise) Human, but even then, if you were a Sorcerer or Barbarian, expect some hatred. It isn't like that in the second game as much, but there is some racism taken for laughs (like Neeshka the Tiefling calling dwarves "squat, smelly drunks" and Kelgar the Dwarf calling Tieflings "backstabbers").
Inphyy in Ninety-Nine Nights has a problem with goblins. Other people fight them and their evil leader. She hunts down their women and children to the dismay of her comrades.
This is what essentially sparked off the story in the Oddworld series: Originally the Mudokons and Glukkons were neighbours, until a crater in the shape of a Mudokon pawprint appeared on one of Oddworld's moons. The Mudokons declared that this was a divne sign that they were the 'chosen race', which royally pissed off the Glukkons to the point of closing off their society, turning to industry and enslaving most of the species on Oddworld, starting with the Mudokons. Congratulations.
In the Onimusha series, humans were created by the demon god Fortinbras for the Genma (who he also created) to prey upon. Therefore, many Genma have an intense hatred and scorn for humans, particularly Guildenstern, who, when he isn't transforming them into new Genma or performing horrific experiments/autopsies (while they're still alive!) on them, refers to them as "maggots" on a regular basis. He loves their internal organs, though...
Overwatch takes place after a massive global war between humanity and the artificially-intelligent Omnics. Racial tensions still brew between the two throughout the world, and some of the playable characters have varying degrees of misgivings towards machines, from simple distrust (Zarya is weary of Genji, even though Genji is a human who had been converted into a cyborg) to full-blown racism (Torbjorn praises the British for poo-pooing on Omnics and reacts with disgust when fighting in Numbani, a city where humans and Omnics co-exist peacefully).
While this gets briefly touched upon in the first Phantasy Star game, and more expounded on in the second, the PS2 game Phantasy Star Universe features this as an apparent plot point (and background story), where the Humans have created CASTs (androids/robots), Beasts, and Newmans to inhabit the Gurhal System with them and serve as labor... but the hierarchy gets inverted quite a bit when the CASTs become the supremacists, the Beasts become resentful and rogue-ish, the Newmans become deeply religious, and the Humans still think everyone can get along. CAST speciesism and racism ensues throughout the entire game.
Subtly implied in Algo here and there, with the Motavians especially; in II, they live in a garbage dump because Mother Brain has terraformed the planet and destroyed their native ecosystem, and by IV, Zio wipes out one of their only two established villages pretty much because he hates them. The Espers are also subject to genocide at the hands of Mother Brain, and over the course of the games become so completely reclusive that other humans on Dezolis don't trust them, even when they're doing their best to save plague victims.
Dr. Nefarious of the Ratchet & Clank series is a robot who hates organic beings and wants them destroyed. However, as shown by the Q-Vidcomics in Up Your Arsenal, he was actually once an organic who went through accidental Unwilling Roboticization at the hands of Captain Qwark, thus making him a Boomerang Bigot.
Most of the faction conflict in Rift seems to be more political and cultural than anything else. However, when it comes to bahmi (who are the descendants of human/airspirit hybrids, and thus extraplanar) it's occasionally played straight: A Guardian NPC in Terminus refers to them as "planetouched abominations," and the phrase "half-breed wind devil" comes up in Shimmersand.
In Rising Angels, there is prejudice between humans and the various genetically-engineered Human Subspecies. The in-game database indicates that it can be in both directions, but most of what we see is from humans. One character in particular, Sol Hackett, is particularly bad in this respect, which causes tension between him and the protagonist — they're old friends, but she wants him to dial it back. Sol does turn out to care about the non-human members of his crew, but he still doesn't stop using Fantastic Slurs.
In Rune Factory 3, protagonist Micah is (eventually) tasked with bringing the population of the human village and the monster encampment together in peace, though it seems that it's mostly the village leaders that are keeping up the conflict. It also seems to be the conflict is mostly between humans and the Unvir (basically unicorn elves), as the human village has four not-fully human residents (two are openly known, one is an Open Secret, the fourth constitutes a major reveal).
The Humans Against Monsters (or H.A.M.) organisation in RuneScape are human supremacists, seemingly believing that humans are the chosen people of Saradomin.
Every single NPC in Ryzom displays this. There are four civilizations and two different factions, and everyone thinks that everyone else is an idiot:
The Zoraï, while they appreciate the help the Fyros have given them in the past, still think that the latter need more guidance and help to calm them down from their fiery nature, don't think too highly of the Matis because of how they disrespect nature with their tree-buildings and worship of the Karavan (the Zoraï worship the Kami, who call the Karavan intrusive), and are, at the very least, utterly perplexed at how the Trykers can be so utterly carefree, childish, and naïve.
The Fyros like the Zoraï if only because they helped them out when they were in trouble but otherwise consider them too uptight, they don't think too highly of the Trykers because of their childish nature, and they utterly despise the Matis because they consider the latter far too expansionist.
The Matis don't mind the Trykers since they're pretty resourceful for all that they're worth, but since they enslaved them a while back most don't think too highly of them, they think the Zoraï are nature-freaks and heretics (again, tying into the fact that the Matis worship the Karavan, who call the Kami, whom the Zoraï worship, demons), and they hate the Fyros for their warlike nature, thinking that it makes them stupid.
The Trykers are pretty chill with the Matis but the fact that they were enslaved by the latter is still a sore spot for some of them, they don't like the Fyros because they're too hot-headed for their own good, and can't stand the Zoraï thanks to the fact that when they needed safety the most during the Great Swarming, the Zoraï barred them from entering their cities, leaving millions to perish.
In Sakura Wars, this is what ultimately drove Erica Fontaine into the Roman Catholic Church, as some people hated her for her spiritual powers which can kill someone later on.
In The Devil's Playhouse, Sam's mild prejudice-slash-Squick towards Sybil's marriage to the Statue of Abraham Lincoln is obviously reminiscent of attitudes towards gay marriage, with him wondering if it's even legal in this state, blanking out when Sybil describes how she and he have sex, and calling their union a 'sin against God'. Played for Laughs, though, and he gets over it by the end.
Sal, a six-foot tall cockroach who used to work as a chef at Stinky's until Grandpa Stinky found out about it, is implied to be something like this, since Grandpa Stinky doesn't have a problem with regular cockroaches in his diner.
In episode 301, Sam asks general Skun-K'ape, space gorilla, if he wants a banana. His reply drips with snark.
Skun-K'ape: I see. Because I resemble one of your earth gorillas, you assume I want a banana. It's nice to see earthlings are still so charmingly racist. Sam: Relax, buddy. We were just making sure you were getting enough potassium.
It seems to be something of a sore spot with Skun-K'ape — it resurfaces in episode 303, when Papierwaite accuses one of his minions of manhandling one of his guards.
Skun-K'ape: They did not, and I would appreciate it if you didn't use speciecist words like "manhandle"! Papierwaite: Oh, take it like a man, you big ape!
Ferals (beastmen) to humans in Sands of Destruction. Sure, there's a few places where they're more or less equal, but the rest of the world? There's a reason why Morte's a part of the World Annihilation Front.
Every Law-aligned characters in the series. They really, really hate demons.
A more humane example appears in Shin Megami Tensei IV between Luxurors and Casualries. The former are the nobles and the latter are peasants, farm workers and overall doing jobs to supply the lifestyle of the Luxurors. The same game also has the inhabitants of Tokyo known as the Unclean Ones to everyone in the Eastern Kingdom of Mikado. The angels take it a step further, calling everyone in Tokyo "Filth". Infernal Tokyo seems to have racism between the Demonoids and the humans who decided to not turn into demons. The latter are also mostly seen as food for the Demonoids.
Lu Cain and the Ze Balmary Empire towards the Earthlings in Shin Super Robot Wars. Eiji asks why Lu Cain persecutes the Earthlings in an Earth Route scenario when Lu Cain is after the Tronium. Lu Cain replies that he's free to dispose of cosmic garbage like the Earthlings however he sees fit.
Happens in Sins of a Solar Empire in the case of the Advent and the TEC. The Advent, when rediscovered by the Trade Union, were reviewed as outcasts because of their beliefs. They were exiled, and now they've come back to get revenge on the TEC.
On a more serious note, Word of God said that Ferals and people who host parasites are looked down upon. Since Eliza was able to hide her's due to her parasite replacing her skeleton, she does not experience the discrimination.
In Star Fox Adventures, the EarthWalkers and CloudRunners "do not see eye-to-eye" for whatever undisclosed reason. The only other bit of info is that Tricky's father says bad things about their queen. Most likely, the EarthWalkers only dislike CloudRunners because they can fly.
The various races of Starbound each have their own little negative history with one another, like the Florans almost eating the Hylotl civilization into extinction, something that leaves the two races in very tense relations to say the least. And on the flip side of the peacekeeping Terrene Protectorate that the Humans created to bring peace to the galaxy, there is Occasus, an extremist organization/fanatical cult of human-supremacists determined to evict all non-human races from Earth and ultimately secure humanity as the dominant species of the Universe. And much like Cerberus they seek to enlist an Eldritch Abomination in the (very mistaken) belief that it will cleanse the universe of all "lower" nonhuman life.
The VUX of Star Control have it in for humanity, and want to wipe them out. Why? Well, they'll say it's because a human called a VUX a "Very Ugly Xenomorph" back during first contact (the VUX are not particularly attractive creatures, it's true). Not entirely true though. The real reason is that, by VUX standards, humans are so utterly disgusting and repulsive that they have to consciously hold back a vomiting reflex upon looking at us. They will even admit that this is unreasonable, that they recognize that humanity didn't choose to look they way they do... but we're just sougly that they can't handle it.
As hinted at with Star Trek: Nemesis, many of the Romulans of the Romulan Star Empire treat the Remans as nothing more than slaves. General Hakeev of the Tal Shiar is more than happen to try to put them down.
The Iconians just hate everyone, complete with the A God Am I mentality.
In Styx: Master of Shadows, although discrimination and abuse is prohibited by the Human-Elf Peace treaty; humans Akenash commonly look down upon elves, calling the elves with various pejorative slangs between themselves, such as "Rootsuckers". After Aaron take place as governor after the death of his father, one of the policies he employ to rally the humans is to "lockup all the Elves (to show the superiority of the human race)".
Much of the plot of Tales of Symphonia involves racism against half-elves on the part of humans and elves. The word "racism" itself is never actually used: the word "discrimination" is always used instead, even when it's just describing racial hatred rather than actual unfair treatment. The majority of the half-elves in the game belong to the Desians, a faction representing The Devil in the Big Bad's made-up religion that subjugates each world in turn to encourage them to do the whole "world regeneration" thing, but it is eventually revealed that half-elves were already hated before the Big Bad set all this up.
There seems to be a level of distrust of people from Mizuho. Ozette too, because they oppose the Church of Martel. (Which is ironic, as that's the place that acts most racist towards half-elves. Pretty much anyone you talk to in Ozette makes a remark about how much they hate half-elves, even the children.)
Half-elf racism seems to be slowly fading away Tales of Symphonia: Dawn of the New World, but in it's place is Tethe'alla and the Church of Martel oppressing Sylvarant, which is seen as a nation of technologically deficient barbarians.
In Tales of Eternia, the Inferian perception of Celestians is of warmongering, bloodthirsty monsters. A library book in Imen reveals that Celestians have only a slightly better view of the Inferians; it was the racist feelings of the Celestians that triggered most of the games events.
Tales of Innocence. A good slice of humanity is gaining powers from their status as reincarnations, and the government is kidnapping them for research purposes. Bonus points: the reincarnatees were having a race war with each other, which is bleeding into the awakened reincarnated humans. A real world war is being thrown into chaos because some of the soldiers have decided to fight the heaven war instead of the Earth war, and the divisions don't always match up.
There's a degree of this in Tales of Phantasia, although it's less central to the plot. It's not surprising, because Tales of Symphonia is implied to be set in the distant past of the same world as Phantasia.
Tales of Xillia 2 has a little of this. Some citizens of Elympios are shown to be rather prejudiced towards foreigners from Rieze Maxia due to their ability to use spirit artes, calling them monsters or even attacking them. Gaius' character episodes revolve around trying to resolve this issue.
Shadowlings in the first game sneer at humans as inferior "fleshlings", though your party members are more tolerant of the Player Character. After their empire is toppled, the new government tries to foster a more welcoming and tolerant atmosphere, but visiting their capital city in Telepath RPG: Servants of God reveals that racism is still alive and well in some sectors.
The racism persists in Telepath Tactics, where the mining company has this in spades. Archos considers the suffering of his human slaves hilarious, frequently mocking them on their inferior thought processes. Tarion is even worse, though, constantly referring to humans as "animals"; he seems to consider them utterly inferior to shadowlings in every way. This is reflected even in his Last Words: "How could this be? Defeated by...mere animals..."
Telepath Tactics also introduces a new non-human species, the lissit, who also seem to experience friction with humans. Silithis Predat constantly insults Emma as a weakling "hesh" ("human", though it literally translates to "hairy thing"), while Bloodbeard's bandits insult Silithis' warriors with taunts such as "Go bask on a rock you scaly freak!"
Rosie really hates the Darcsens often taking out rage her on Isara. Rosie does have a Freudian Excuse for this, as revealed in her "Report" chapter; when she was a child, her family was killed during a raid on their Darcsen neighbours. She grew up blaming the Darcsens for it. She eventually comes around and stops hating Darcsens.
There are a few other playable characters who also hate Darcsens, but unlike Rosie, this comes in the form of a potential that lowers their accuracy when they're near allied Darcsen. Rosie, meanwhile, learns a potential that actually improves her accuracy when near Darcsens, although she only gets it after Isara's Plotline Death.
Darcsen-hating is institutional in Europa, especially in the Empire (which is happy to round them up, burn their homes, and send them to work camps). In Varrot's side mission, Geld is court-martialed "for torturing non-Darcsen civilians." Another mission has you visiting a Darcsen concentration camp, where they are worked to death by the Empire and a large number are executed as you attempt to liberate it, if the Darcsens being expies for Jewish people wasn't Anvilicious enough already.
The Valkyrur themselves are subject to this, despite being extremely rare. Once we find out they're responsible for the Darcsen calamity, anyway, and most of Alicia's problems come from what is essentially internalized racism.
The sequel Valkyria Chronicles II makes racism a bigger plot point as the antagonists are a Gallian Noble House that didn't take well the whole revelation of Gallia's ruling family being Darcsens.
Wild ARMs 5 has this trope as its Anvilicious morality tale - the tall, beautiful Veruni constantly oppress the smaller, weaker humans, while the protagonists work tirelessly to prove The Power of Friendship and how we're all really the same inside. Unusually, this is because they are - the Veruni used to be humans long ago, before they left for space.
This is part of the reason for the hostile relations between Horde and Alliance after they formed an alliance against the demons in Warcraft III. When these mentalities were toned down in the Burning Crusade expansion, players complained. Cue a 180' turn in the Wrath of the Lich King expansion, where fueling said racism is a part of the Big Bad's Evil Plan.
This is all over the place in the backstory novels. For instance, in the first war against the demons, the night elf nobles initially refuse to accept the help of other races (at that time, dwarves, the ursine furbolg and the tauren), and the demons manipulate the orcs into fighting the draenei by fueling the mistrust.
Grand Marshal Garithos from the Frozen Throne expansion is probably the biggest fantastic racist in the series. His comeuppance was exquisitely satisfying because of it.
In an interesting take on this trope, you'll find plenty of "racism" in the player base against Gnomes and Trolls.
The Horde counterpart is the Blood Elves, who are the only "pretty" race among the Horde. And considering that the Blood Elves were added in the Burning Crusade expansion, Suffers Newbies Poorly is probably a contributing factor.
Some built-in emotes are racist. This is a /silly from human males: "So, an orc walks into a bar with a parrot on his shoulder. The bartender says 'Hey, where'd you get that?' The parrot says Durotar. They've got them all over the place!'" And this from undead males: "I can't stand the smell of Orcs."
The Forsaken have a general contempt for all races other than their own, even the Tauren who have a genuine desire to cure their undead state. They start off as Neutral with all other Horde races, whereas others start at Friendly. The Forsaken have a particular hatred for humans as a result of their forced conversion and the disgust of their former friends and family to their undead states. A set of now removed quests in Alterac Valley, involving two brothers, one Human and one Forsaken, sent players to kill their own brother.
It's near impossible to find a Orc that isn't racist against humans, due to imprisoning them after they lost a war, many forced to grow up in concentration camps for crimes that they didn't understand. Many were mistreated, and all were generally looked upon as no more than caged beasts. After Thrall and Grom set most of them free and they resettled in Durotar, the Kul Tiras fleet attempted to commit genocide against them for the crimes of their parents, even though the Horde had been freed from the Demonic corruption.
A lot of the Blood Elves' emotes are racist against their own faction: "We're allied with the Tauren? Fantastic! We'll have steak every night!" and that really long one that the female blood elves have about the undead.
There is a blood elf vendor in the belf-starting-zone that refuses to sell to trolls and insults them when approached. Someone should tell him that Vol'jin sent troops to help against the Amani, though the whole zone is stuck in bc.
The Blood Elves get a truly ridiculous amount of hate. The High Elves of Dalaran rebelled when Rhonin considered allowing Blood Elves back into the Kirin Tor. High Elves and Blood Elves were once the same race, but ~10% of the remaining High Elves didn't agree with Kael'Thas and didn't become Blood Elves and instead stayed loyal to the Alliance. The high elves consider the Blood Elves traitors and refuse to have anything to do with them to the point where no high elf would ever wear red because it's the color of Blood Elves.
Varian Wrynn does not like orcs very much. In the novel Wolfheart, he also expresses contempt for the worgen. However, in a bit of a subversion, it's not the worgen he has contempt for, it's the fact that all the worgen he knows are Gilneans, who went into isolation following the Second War and did nothing as Alliance kingdoms were being destroyed by the Scourge and the demons. By the end of the novel, his opinion of Gilneans radically improves, especially after he personally leads them to turn the tide in a major orc offensive.
Cataclysm has Garrosh kicking almost all of the other Horde races out of Orgrimmar. He allows trolls, goblins and tauren to live in the city, but in crappy slums on the outskirts. At one point, Garrosh tells Vol'jin, the much more experienced leader of the trolls and somebody who, before Thrall left, was in a higher position than Garrosh, to return to his slum. Garrosh's attitude towards non-orcs come Mists of Pandaria can be summed up thusly: If you follow every single order you're given (including idiotic and/or suicidal ones), you're expendable. If you refuse to follow any order, you're a traitor to be executed.
In Northrend, there are very few Draenei among the Alliance forces; a recurring discussion in Valliance Keep reveals that most of the Alliance forces are from people native to Northrend, who up until now have never seen a Draenei, and are suspicious of them. Harbinger Vurenn suspects the Cult of the Damned is deliberately stoking this to weaken the Alliance forces.
The Mogu in Mists of Pandaria believe that all other races exist solely to act as slaves to the Mogu.
The Witcher has this as a major theme of the game. Both the humans and the non-humans (elves and dwarves) display this, which leads to armed groups like the religious fanatical Order of the Flaming Rose and the terroristic Scoia'tel to commit horrific atrocities against the other race. Geralt himself is also a target of the racism.
In The Witcher 3: Wild Hunt, a major plot point is Radovid's insane hatred of people who use magic, brought about by being betrayed by the sorceress Phillipa Eilhart. Novigrad is gripped with a witch-hunting craze, driven by the city's Corrupt Church. Healers, alchemists, and even simple fortune tellers are dragged out into the streets by fanatical witch hunters, where they are arrested and beaten, the hunters seize their homes and their property and burn any and all "unorthodox" books or magical items they find. The Lodge of Sorceresses has fled for their lives - Keira Metz is working incognito as a white witch out in an isolated village, and Triss is still in the city, operating an Underground Railroad for magic users. Eventually, the whole city goes into full-blown Holocaust mode and begins rounding up all magic users to slaughter them. If Geralt helps Triss to evacuate all the surviving magic users to a ship heading for Kovir, about 30 in all, then the church then begins targeting non-humans.
Xenoblade Chronicles X: As aliens begin living with and integrating into New Los Angeles, racial tensions begin emerging among the citizens. While the NLA government is officially open to new treaties and alliances, and most humans are rational enough to know that more allies and friends can only be a good thing in the situation they're in, some are shown with an extreme hatred of all "xenos". Some of them do nothing more than grumble about it, a few bigots can be convinced of their jerkassery and make an effort to come around, while others take it to such a level of hatred that they start attempting to "cleanse" the city of aliens.
Half the point of the Zone of the Enders series. In fact, "Ender" is a pejorative term by Earthlings referring to those born on Mars and the outer colonies. In turn, the Martians use it for those living on the outskirts of the solar system.
The humans in Mega Man Zero 4 are shown to be very distrustful of Zero and reploids in general. Though to be fair, reploids did spend over 100 years destroying the planet during the Maverick and Elf Wars, not to mention all the propaganda against "Mavericks" (of which Zero was almost certainly vilified in) the residents of Neo Arcadia were subjected to, and the fact that Zero killed Copy X, one of the few reploids the humans still trusted.