Pretty much every race hates every other race in Above Ground, and there's the human/infected hatred to go on top of that.
The third chapter of The Account introduces Alan Ruby, an accidental human visitor to a gas station in a diverse world of fantasy races. He freaks out, starts lobbing the word "monsters" at the goblins and gnolls around him, and gets smacked around for it. Earth-born humans face their fair share of prejudice as well, but there's a reason for that...
Adylheim treats this as a little more complex than most examples of Fantastic Racism do. Every race - even the human races! - is treated according to different stereotypes, some of which would at first glance seem to be positive. For example, the dragonkin, anthropomorphic dragons, are very rare in Adylheim, and it's considered good luck even to see one; but though this is a more "favorable" stereotype than any other race has, it also leads to them being harassed for favors at every turn, resented when they "won't" perform small miracles, and sometimes kidnapped and held to prevent their good luck from escaping or murdered for their body parts.
Orange, from The Annoying Orange, doesn't seem too fond of apples. In the show, he would often tell other fruits and vegetables that they were being apples. Though, this could be Orange being his usual dim-witted self.
ARCHON plays with this: Arglwydd repeatedly makes references towards Joule, the only human member of the group, as a dog. Both Averted and Played Straight within the lore: it is mentioned offhandedly by Jager that although discrimination isn't permitted within the Holy Kingdom and the Elven Lands, other nations are no-where near as fair.
In the online speculative evolution project A Scientific Fantasy, dinosauroids, humans and goblins don't seem to get along very well. However, they're treated like religions rather than races, seeing as dinosauroids offer humans as sacrifices and goblins worship a god called Allah.
Also, an Austrian elf named Hister is Omnia Sanatem's version of Hitler, having started "the Great War", put people in concentration camps, and killed 6-16 million.
In The Gamers Alliance, the anti-elven movement in Remon gets so bad that humans pretty much hunt down any elves they can find and vice versa until the dark elf Mori'sul finally manages to calm things down. The Sarquil tribes of Libaterra use dark-skinned desert elves as slaves and kill any lizardmen they can find. Demons see all non-demon races as inferior which in their view justifies that they can use these "lesser races" as slaves and food.
During an encounter with centaurs in Greek Ninja, one of them reveals to Sasha that the founder of Ariadnio was a protector to them from humans, suggesting that there is racism towards centaurs.
MSF High Forum: Legion get this, a lot. GAN get this sometimes, and the AP tend to have this against everyone.
Reverse Jurassic Park: The Velociraptors (except, naturally, Mr. Robustus) find that keeping a Dilophosaurus in captivity is unethical because he is as smart as they are, yet they have no problems with keeping humans in pens.
Shows up in RWBY between humans and Faunus (who have animal characteristics). It doesn't appear to be an institutionalized thing—a Faunus openly attends Beacon Academy—but humanity is clearly on top and many humans (such as members of team CRDL and Weiss) view all Faunus as being dirty, criminal, freaks, and terrorists.
After Hell was conquered, it was mentioned that the demons had to be guarded mostly to protect them from the humans they have tortured.
In 'Souls RPG, the coyotes of Inferni are racist against wolves, and the packs New Dawn and Sangilak only allow wolves.
Done well in Tales of MU, which examines the prejudices of both human and non-human characters, which sometimes skirts right up against stereotypes like Noble Savage and Humans Are Bastards, but ultimately averts them by showing all sides warts and all.
An interesting example of this is the character of Steff, who, as a half-elf, has had to deal with the prejudices of elves and humans against each other (mild though they are compared to the kind of treatment Mack generally receives when people discover she's a half-demon). This, consequently, has caused her to express racist opinions towards both, thinking of humans as clumsy clods and elves as stuck-up assholes.
A blatant example of anti-nonhuman bias in the story is the assumption that nonhumans at MU prefer to be called solely by their first name and the appropriate honorific (with female nonhumans generally referred to with "Miss" rather than the typical "Ms."), rather than their last name and honorific. This is despite whether or not the nonhuman actually has a surname (supposedly this is done to respect the fact that some races don't use surnames). When Mack tried to politely request that one of her professors refer to her as "Ms. Blaise" as opposed to "Miss Mackenzie", a fellow student's reaction was essentially to question her sanity.
Several times in the story characters have pointed out that the entire concept behind Harlowe Hall is inherently racist: there's no reason why a goblin would get along better with a mermaid (for example) than she would with a human.
One of the lynchpins of the Tasakeru universe. The eight sentient species are all vastly different from one another, and warred with each other constantly in centuries past. A truce was only established through the divine intervention of the three Gods that inspired sentientkind to live together. Unfortunately, once the Gods became ingrained into each culture, the tensions rose again. The only way that harmony could be maintained was by walling off the species from one another. Tempers still run high between them... the only real unifying factor is that everyone seems to hate the cross-bred wolfoxes. It's seen as socially acceptable to either ignore them or use slurs like "stains" to refer to them.
Sam Bak Za'z "There she is!!" series gives cats and rabbits a dynamic with parallels to black/white interaction post emancipation. It's more enlightened in that neither species has anything in particular against the other and they get along okay, but romance between the two is so frowned upon that they actually have signs posted around the place just to remind people about it.
Sam Bak Za are Koreans. The series is more about relationships between Japanese and Koreans. There's still a lot of hostility between them today, holdovers from historical rivalries. Same deal, though.
In the web novels of Trinton Chronciles lizards and dragons are treated with both awe and fear by the rest of the mammilian populace.
Ultra Fast Pony gets a lot of awkward laughs out of Ponyville's rampant racism. They hate and fear other species (griffons like Gilda and zebras like Zecora), and they hate blue ponies. ("But Rainbow Dash is blue!" "We hate her, too.") Enslavement of pegasi was (and possibly still is) widespread. In one episode, Pinkie Pie volunteers to sing "the traditional song of the buffalo"; her song starts with the lyrics "Oh I'm a dirty brown buffalo!" and gets worse from there. Nearly all of these play out with references to Real Life racism: for example, Zecora is a Jive Turkey, and Fluttershy is a Steppin Fetchit whose only moment of showing backbone involves telling another character they're not allowed to say "pegger". Twilight tries to call the other ponies out on their racism, with limited success.
Given the mishegas of strange species and mutant humans prevalent in the desultory plot, it's surprising that Welcome to Night Vale subverts this. when Hiram McDaniels (five-headed dragon, eighteen feet tall, breathes fire, in jail for insurance fraud) announces his intention to run for mayor, it's not the "five-headed dragon" part that people care about...it's the fact that he's in prison.
Cecil: Now, isnít it just like a career politician, such as Mayor Winchell, to make such unethical, ad hominem attacks on a great reptilian beast, simply because he is in jail?
Double Subverted later, when Cecil accuses the current mayor of being racist for insisting that a dragon can't be mayor and not giving any further justification than that.
Of course, McDaniels himself seems to hold some...interesting view-points of single-headed species, repeatedly calling them 'sacks of flesh' and constantly insulting their intelligence.
All over the place in the Whateley Universe, where a huge number of baseline humans hate or fear mutants and their powers. There's a The Men in Black-like organization called the Mutant Commission Office that tracks (sometimes abducts, and possibly murders) mutants. 'Humanity First!' is a popular anti-mutie organization that has groups all over the world.
The Triarian Collective and Equestrian Empire in Void Of The Stars. Somewhat justified as the Triarian Collective is oppressive and dystopian, and the Equestrians stole Triarian genetic material to create a slave subspecies.