Anti-Human Alliance

All right, you know the drill: Two or more groups of aliens really hate each other not for concrete differences but over Fantastic Racism. Cue a new kid on the block that threatens both. Cooler heads prevail and they team up against the new guys, in the process they learn a valuable lesson about tolerance and embrace The Power of Friendship. Pretty standard plot and Aesop, except for one tidbit. The new guy? That's Humanity. Either because of real or perceived threat, these alien races have banded together into an Anti-Human Alliance with the goal of either conquering and enslaving us or outright wipe us out of star-charts.

Despite the space focus, this trope can be used in any setting with one or more non-human races. In Fantasy it's usually a group of evil races such as orcs, goblins, undead, etc. However "good" fantasy critters may despise humans for their own reasons, such as fairies, elves, dryads, etc. It's especially common to have post-humans form such an alliance, such as Mutants, Cyborgs, vampires, and people with superpowers. Better yet, the non-humans that want to kill humanity are its children, such as rebellious robots, AI, and Designer Babies.

The motivating factor behind this alliance can vary, here are a few common causes:

Humans taste really good, so enslaving us en-masse is in their interest.
They see us as a threat to their empire or race.
They are Fantastic Racists who consider us inferior and weak, fit only to be wiped out.
They need slaves for the ice mines on Chiron Beta Prime.
Humans treat them as delicious/worth enslaving, so preventive genocide is on the table.
Humans have exhibited Fantastic Racism on them, potentially trying to wipe them out or enslave them.
They were once human and want to lord it over the rest.

Depending on the tone of the series, these differences may be resolvable or ultimately lead to endless war and conflict until one side finally kicks the bucket. It's also worth noting that humanity may have one or two non-human allies that are being equally targeted for helping us out.

Examples of Anti-Human Alliance include:

Anime & Manga

In Princess Mononoke, apes, boars, and wolves don't care at all for humans. The apes want a more limited war. The boars argue for a more all - out war because it's Better to Die Than Be Killed. The wolves end up siding with the boars more out of sympathy than anger.
In Rosario + Vampire the monsters (at least several, if not dozens of species) have united to create a monster world separate from Earth, and exterminate humans who sneak into the monster world. Much to his chagrin, Token Human Tsukune finds himself mistaken for a monster and gains a Cute Monster Girl Five-Man Band Unwanted Harem, at least some of whom believe Humans Are Bastards. His True Companions choose to stand by him when his cover is blown, fending off a small army of their classmates.
Done by Optimus Prime/Megatron expies in Panty and Stocking With Garterbelt - the eponymous characters kill them when they arrive on Earth, and they merge into a single powerful Ghost that wants to wipe out all humanity (after making peace with each other).

Comic Books

In DC Comic's Crisis Crossover "Invasion!" various alien races are convinced by The Dominators to help them invade Earth, out of fear of its superbeings- and disgust over our genetic variety. Of course, The Dominators all along planned to capture the superhumans and use them to conquer the universe.
Marvel Comics had a similar crossover in which Earth was sealed off from the rest of the universe for having intervened in the affairs of other civilizations too often (nevermind that it was often to save them). They even dumped their alien criminals on our world! (As in Invasion! this turned to be part of a plan by one race to then turn on the rest.)
- Speaking of Marvel, um, the Brotherhood of Mutants? Though to be fair, humans started it.
The Superman arc that reintroduced the "retroboot" Legion of Super-Heroes features the United Planets going to war with the xenophobic Earth.

Film

In the Hellboy II backstory, humans are at war with elves and the other magical races, nearly driving them to extinction. This prompted the elves to create the Golden Army, which decimated the humans so badly that the elven king was horrified and negotiated a peace.

Literature

In the Star Wars EU Young Jedi Knights, there's the Diversity Alliance. Who plan on killing humans with a bio-weapon that only targets humans.
- Far earlier, there were several anti-human resistance movements on Coruscant, mostly in reaction to the oppressively human-centrist government.
Sergey Volnov's Army of the Sun is set after a galaxy-wide rebellion of alien races against the EarthStella Empire, which had formerly conquered all of them. All the aliens join together to wipe out the human threat. Of course, no side is in the right here. This is a Crapsack Universe, after all.
In The Stainless Steel Rat Wants You, humanity is attacked by a coalition of alien races hell-bent on wiping out all humans simply for looking ugly. Their only similarities are that they're all slimy, ugly (from a human point of view), and reptilian/amphibian.

Live Action TV

The Alliance in the Mirror Universe in Star Trek: Deep Space Nine is a coalition of races that rose to power in the vacuum created by the Terran Empire's decay into a more democratic and peaceful organization after Kirk made some convincing arguments about mercy and compassion to Mirror-Spock.
- Before that (in-universe chronology), there was the Anti-Imperial Alliance in Star Trek: Enterprise.
- According to the non-canon Shatnerverse novels, it was Tiberius himself who manages to convince the Cardassians and the Klingons (who hate each other) to join against the weakened Empire, after Spock ousts him. Then they pull an You Have Outlived Your Usefulness on him.
- There are also the Xindi, who are hell-bent on eliminating humanity. While they're all originally from the same planet, they are five (formerly six) distinct species.

Video Games

Halo has for antagonists a collection of different alien species under the banner of religion, whose aim is to wipe humanity from the face of the universe because they're unholy. Well that's what the common Covenant grunt believes at any rate.
- Subverted. By the end of Halo 3, only the ones loyal to the "Prophets" are still trying to wipe humanity out. Those who had been betrayed by the Prophets or simply disagree with the Covenant religion becomes allies of the humans.
This is the plot of Icewind Dale II, the two Big Bads gather all the monster races bullied by the six towns in the north for their savage behavior (the monsters', that is) and put them under one banner.
Two of the races in the Horde of World of Warcraft fit. The orcs were once enslaved by humans, and most Forsaken were once humans. Many humans in the Alliance would very much like to see both of these groups destroyed because of what others of their race have done.
- The blood elves are another example. They used to be part of the Alliance, but a racist human leader decided to betray them before they could betray him. This set off a series of events that led to them being new members of the Horde.
The Scoia'tael in The Witcher is an alliance formed between elves, dwarves and a few other fantasy races, who commit acts of terrorism against humans in retaliation for the Fantastic Racism humans subject them to.
The Fomors in Mabinogi and its prequel Vindictus see humans as a menace to the world (all that chopping and building and domesticating—such greed and hubris!) and want to exterminate or at least ruin humanity. The Fomors accept anyone who wishes the end the human threat, even disillusioned human renegades.
In The Elder Scrolls series, both before Tiber Septim's rise to power and after the fall of the Septim Dynasty and the beginning of the Fourth Era, the Summerset Isles (the Altmer) and Valenwood (the Bosmer) were a unified nation known as the Aldmeri Dominion (which is decidedly anti-human in its overall stance). Before, Tiber Septim used a massive golem to conquer it. After, as of the books (which are set 160 years before Skyrim, and this section MAY need to be revised when new information from Skyrim dumps out), the Dominion is in direct conflict with Titus Mede's reborn Empire. Given the lore of the Altmer (who are the dominant partner in the Dominion), it would stand to reason that they are quite decidedly anti-human in stance, even if the two power blocs are powerful enough to discourage open war.
If you played the Renegade path in Mass Effect 1, the Citadel species become a lesser version of this in 2: they aren't openly hostile to humanity, but they resent humanity's quick rise to power and the implication that Shepard deliberately threw the Battle of the Citadel in order to kill the Council.
Subverted in the Winds of War expansion of Heroes of Might and Magic 4 - The other factions have specific and very different reasons for fighting the humans, and are fighting each other over which one will eventually conquer them.

Webcomics

In Order of the Stick, Redcloak's goblins & hobgoblins fight alongside Xykon's undead against the mostly-human Azure City. Redcloak may be a Card-Carrying Villain, but he and his forces are also fighting their right not to exist only to be killed for Experience Points. On the other hand, Xykon's fighting to accomplish his current Evil Plan and For the Evulz.
In Goblins, there's a generalized conflict between the humans and their allies (dwarves and elves), and creatures such as goblins, orcs, ogres, etc. The main reason for the conflict seems to be Fantastic Racism on part of the humans, most of whom aren't very bright.
In Drowtales, the multi-species adventuring party takes on the human kingdom after the king orders all beings of elven descent arrested. However, Lady Ariel is fighting only to rescue Faen and her companions are mostly just trying to keep her from getting herself killed.