Fantastic Racism/Web Original

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.
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 off-handedly by Jager that although discrimination isn't permitted within the Holy Kingdom and the Elven Lands, other nations are no-where near as fair.
This is the subject of one of Furry's Vlogs on Transylvania TV
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...
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 the Real Monsters, 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. It's implied that the reason the Leightons behave the way they do is because they've been forcibly put with individuals they have nothing in common with because their bodies were fused together.
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.
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.
Oxhorn Short Shorts takes this trope and sprints around the line with it. The main cast(s) are all Horde, and their sentiments against various Alliance races are stated and stated often. (Not Counting the Orcs In Space series,) there is scarcely a film that doesn't bash elves, gnomes, or common World of Warcraft player types, sometimes in song. To be fair, all elves are portrayed as hippie Camp Gay pricks, oftentimes the antagonists. They even go so far as to kidnap Oxhorn (main guy) in one of the holiday specials (Although it is because of the racism).
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.
Pretty much every race hates every other race in Above Ground, and there's the human/infected hatred to go on top of that.
In the Darwin's Soldiers universe, Snakes are considered to be repulsive by other species.
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.
In the web novels of Trinton Chronciles lizards and dragons are treated with both awe and fear by the rest of the mammilian populace.
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.
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 rahter than races, seeing as dinosauroids offer humans as sacrifices and goblings 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.
Several of the demon species in The Salvation War were held with disdain by the more major "races," such as the Gorgons, who can do about anything, but far worse than any of the more specialized species. Orks (which were the original residents of Hell) have been reduced to slave labor. Humans were (in more ways than one) just food for the demons.
- 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 RWBY, the human population of the world of Remnant tend to treat the Faunus as second-class citizens at best, and as animals at worst.
J.F. Sargent of Cracked.com calls the very existence of Fantasy Counterpart Cultures one of the "5 Prejudices That Video Games Can't Seem to Get Over".