Hogyoku Ex Machina has a meeting with Yamamoto, Ukitake, Kyoraku and Unohana where they discuss how the (now dead) Central 46 were xenophobic pompous pricks to the Vizards and had them exiled. They then agree that if they can't remake the Central 46 with people who avert this then the Vizards and Ichigo (since he's one of them) will have a valid reason to hate and destroy Soul Society. They generally do this to make peace with the Vizards and not prompt a God Mode Ichigo to come after them.
In the Jackie Chan Adventures and Teen Titans crossover fic A Shadow Of The Titans (part of Project Dark Jade) Suzano is a Jerkass with a great hatred of Jade, which he claims is due to her being part Oni while he claims to be descended from a Japanese god of the same name. But after it is revealed that he is on a team with a ghost and a demon, and that he also has racist feelings towards the very human Gadjo, it is suggested that he just uses it as an excuse to be rude to people.
The Warmistress of Equestria; the deer see almost all of the other races of Equestria as beneath them, although the one most vocalized is towards ponies; they consider ponies to be backwards, short-sighted brutes who would try to exploit or destroy the deer.
A Discworld "South Africa" has been introduced in Fan Fiction, which combines both the "mundane" racism inherent in apartheid with the "fantastic" racism of the Discworld - for instance, Igors are not appreciated in "Rimwards Howondaland" because they have a terrible habit of matching serviceable parts from black-skinned people to white-skinned people who, well, need serviceable parts. This is held by the authorities to be a seditious plot to bring apartheid into disrepute.
Cid: Though it is not as widespread as in the past, there are still those out there who believe in racial hiearchy. Humeism is one of these. It seems they picked up on the Archadian's sense of Hume superiorty.
In the unrelated Queen Of Shadows, it's shown that there is no love lost between the humans and Shadowkhan in Feudal Japan. Though it's unknown whether this was the case before the Shadowkhan started conquering the country one island at a time.
Mass Effect has its own prevalence of Fantastic Racism, but Mass Effect Human Revolution takes it even further. Anti-Aug discrimination is practically government policy, and the the anti-Aug cult "The Order" is the most widespread religion. Adam Jensen's heroic defense of Elysium is glazed over by Alliance propaganda, simply because he's considered a pariah now. Even other races discriminate less against Augs than humans. Quarians fare worse in this universe, as the Order hates them for creating the geth.
In All-American Girl due to a very bad first-contact situation humans and ponies have plenty of mistrust between them even twenty years later, reflected in slurs. While the ponies have been rather tame in their epithets of humanity ("monkeys" are the worst that's been said), humans, on the other hand, have been a bit more colorful:
Lyra: “Let me see if I can recall some of the speciest slurs made about ponies: Kickstands. Tugs. Geldos. Roadshitters. Cathyfuckers – I don’t even know what that means.”
In recent chapters, the ponies are becoming more creative in their slurs towards humans such as "Skinners"
Fantastic Racism and race/species relations are certainly among the major themes in Citizen Weevil, in which a changeling family, amongst thousands of others at a time of mass migration, have immigrated to Equestria and are now living in the Six Points, a deprived multi-species district in Lower Manehattan where there lives ponies, changelings, diamond dogs, griffins, etc. Although, unlike many other MLP fanfics discussing racism, the majority of cases are that of casual and institutional racism and cultural clashes instead of full on oppression as these are immigrants legally allowed entry into the country.
Largely in a meta sense in The Conversion Bureau and related works - ponies constantly and unendingly deride the works of man, and the authors are on their side.
Celestia used this to unite the pony tribes in Diaries Of A Madman, after her previous plan backfired.
In Fluttermom, Empyreanists are a group of Pegasi who believe that any species that cannot fly is inferior. The author has specifically referred to them as the pony KKK.
Lots between Unicorns and Earth Ponies in Captain Equestria. The latter are referred to by less savory characters as "diggers" and are treated like second class citizens, which of course inspires a lot of hate back the other way.
Diamond Dogs are seen as idiotic brutes. Rarity is quite surprised at how intelligent Kili is.
Trixie doesn't think much of thestrals (batponies, who are the dwarves of this universe), at least not enough to approve of her son marrying one.
In My Little Unicorn members of Starfleet tend to point out quite often, how much superior they are compared to Equestrians.
There's many Friendship is Magic fanfics involving Fantastic Racism between griffons and ponies, one in particular is in Summer Days And Evening Flames where Gilda is called a "half-breed" by a pegasus.
Ubiquitous in Under The Northern Lights. Ponies about reindeer, reindeer about ponies, the zebra Paki abouth both categories, etc. In many cases it is not just mutual prejudice, it is also relatively low-key and consists of misunderstanding and underestimating the other, rather than outright oppression. The latter happens, though. Reindeer treat the Russ (immigrant dwarf Earth ponies) and the Urox (native aurochs) as second-class citizens, and we learn that ponies used to do the same to cattle, sheep and so on, who used to be slaves. Not everyone is racist over the board, either: the pirates of the Crimson Kraken are happily multi-cultural, but have a very negative view of "primitives" like the reindeer and the ponies from Tropical Island.
What Hath Joined Together sees Equestria using a Fantastic Caste System with social standing depending on race. For the most part, it's restricted to job and marriage opportunities and different races are still encouraged to get along, but stepping outside of your races' privilege is a faux pas at best and an actual crime at worst.
In With Strings Attached, Ketafans treat elves like second-class citizens, and Baravadans are supremely contemptuous of Ketafans, which creates friction when the Baravadan Brox and Grunnel must ally with some.
Ironically, most Ketafans think Baravadans are the Favorites of the Gods.
A recurring theme in the Transformers fanfic A Child Shall Lead Them — the Autobots regard the Dinobots as stupid, violent, and animalistic, and treat them as such. This is especially problematic given that one of them (Swoop aka Pterodactus) has ended up with the Matrix after Optimus Prime's death... Pterodactus ends up calling the Autobots out on it, delivering a blistering What the Hell, Hero? speech that shames them into accepting him as their leader.
The Tron-universeFan FicThrough A Diamond Sky plays with the tension between Programs and Isos. Programs see Isos as having no purpose or function, taking up valuable resources and contributing nothing back. Isos see Programs as inherently hostile and constrained by their hard-coded directives.
Flynn:"For a world of ones and zeroes, it annoys the hell out of me how much User-style problems you've picked up...First time I was here, it was persecution based on belief...now this place gets racism, too...You'd think there'd be a way to code out that crap."