The Anti-Spiral in Tengen Toppa Gurren Lagann, follow an eternal mission to wipe out all sentient life to halt evolution forever and prevent the Spiral Nemesis from coming to fruition, going as far as to lock their bodies away and take on a collective consciousness through a twisted silhouette.
Gah Lak Tus, the Ultimate Marvel Galactus, is a fleet of killer robots motivated by a thorough loathing of all organic life; they don't just try to kill everything fleshy, they do so in the most hideous and painful ways they can come up with.
Oddly enough, this loathing is almost completely irrational. The moment Professor Xavier tries to make contact with it, it spasms with revulsion and opens fire on Earth. In the end, they defeat it by giving it a fit of horror at being mentally contacted by the entire human race. Oh, and they also shoot it with a BigBang for good measure.
The Termight in Nemesis the Warlock is on a perpetual crusade to wipe all non-human sapient life from the galaxy.
The Daxamites of The DCU are a ridiculously xenophobic society. They ban space travel, indoctrinate their children with fears of aliens, and teach them that Daxam is their entire universe. Green Lantern Sodom Yat was a rare exception. His own parents had to brainwash him to rein him in, which backfired immensely when he broke free of it. He even chastised his own people for not getting outside help when the Sinestro Corps invaded Daxam.
In Superman's, Kryptonians were another example from The DCU. While they weren't xenophobic to the same genocidal extent as their distant cousins, the Daxamites, they did look down on other species, and they, too, banned space travel research. That ban on space travel is why there are so few Kryptonians left — when Krypton blew up, most of the people had no means of escaping the planet. The only survivors were either stuck in a prison dimension, trapped in an off-world miniaturized city, or sent away in experimental, illegal spacecrafts.
It's actually worse. The Kyptonians were all affected by the Eradicator (which is a genetic enginering project, an AI and a bunch of other things, it's complicated), the upshot of which was even if they found a way off the planet they'd just die.
Sergeant Preus of the Superman storyline Godfall takes this to new heights, desiring to exterminate all of Metropolis for the unforgiveable sin of not being ruled by Kryptonians.
In Runaways, while the Gibborim may have needed a pair of aliens to form the Pride, they later reveal that they despise aliens. They treat Earth as a holy temple to their "Father" (heavily implied to be God) and condemn Xavin (a Skrull) for "desecrating" it with his presence.
The Dyson Primes from Peter F. Hamilton'sCommonwealth Saga are the definition of this. Primes exist as sentient, immobile "immotiles" and sub-sentient motile servants that can merge to create new immotiles. Immotiles control vast armies of motiles and battle each other for resources and out of instinctive paranoia, since their biological imperative for perpetual expansion means they'll always clash sooner or later (and prefer it being sooner). You can guess what happened when they started building nukes. Also, the moment one of them (Morning-Light-Mountain) discovers wormhole technology, it exterminates all others and starts building a vast fleet in order to kill off every single living thing in the universe other than itself, not capable of comprehending the notions of sharing and coexistence. In its own words: "There is only one Universe and it can only contain one life. Me." These guys had gone so far as to exterminate every plant and animal life form from their own homeworld other than themselves and their food crops.
The Ryall from the Antares trilogy are a classic example of the instinct-motivated Xenophobe: throughout their early development, they were preyed on by another sentient species, until they went to war and wiped the egg-eaters out. They see other intelligences only as competitors, and feel a deep need to kill them all.
One of the classic examples of this are The Foe or The Kugel from Fredrick Pohl's Heechee series. Not only do they seem to hate all other lifeforms, they are actively trying to destroy all matter in the Universe. As it turns out, however, they are perfectly willing to allow matter-based lifeforms to exist once a human convinces them that ascending to a pure energy (and thus immortal) state is highly desirable to both the Human and Heechee races.
The Achuultani of the Empire From The Ashes novels have been quartering the galaxy for seventy million years, exterminating every sentient species they can find because they believe every other sentient species would do the same to them. In their case, it's because they've been manipulated by their rogue AI overlord, who uses the ongoing state of emergency as an excuse to keep itself in power.
The Shirmaksu (or Kangas) in The Apocalypse Troll come from the same situation as the Ryall above, reinforced by a religion which holds that God made them in His image and all other intelligences are demons in disguise.
The Gbaba from the Safehold series appear to be instinctive Xenophobes, though we have yet to fully understand why. One character speculates that they've lost their sapience and are governed entirely by instinctive behavior.
John Ringo's Posleen from the Legacy of the Aldenata series are this way, although they are so primative that it's more that they are locusts destroying everything in their path than actually hate filled monsters. The end results are essentially identical however. They are, however, clearly inspired by David Weber's Achuultani, since both are Absolute Xenophobic sentient crested centauroids who rely almost entirely on their computers and attack in overwhelmingly massive swarms. Also, members of both races prove to be willing to listen to reason and, upon setting up their new, less omnicidal society, adopt new names and become allies of Humanity.
The Krikkiters in Life, the Universe and Everything were initially unaware that there was a universe beyond their solar system. The discovery was a major shock to them. As a result, they are absolutely charming, pleasant, decent ... if whimsical ... people whose attitude towards not just life in the rest of the universe but the rest of the universe itself can be best summed up in the phrase "It'll have to go." It turns out they were manipulated into this by the supercomputer Hactar, which had been atomized when it refused to construct a bomb that could destroy the universe. It eventually changed its mind and created Krikkit's xenophobic culture so it could rectify its "mistake".
They flew out of the cloud. They saw the staggering jewels of the night in their infinite dust and their minds sang with fear. For a while they flew on, motionless against the starry sweep of the Galaxy, itself motionless against the infinite sweep of the Universe. And then they turned round. "It'll have to go," the men of Krikkit said as they headed back for home. On the way back they sang a number of tuneful and reflective songs on the subjects of peace, justice, morality, culture, sport, family life and the obliteration of all other life forms. — Douglas Adams, Life, the Universe and Everything
The Pitar in Alan Dean Foster's Humanx Commonwealth novels appeared nearly human, and held out a cautious hand of friendship at first...but this concealed a species-wide psychosis that drove them to attempt to wipe out humans, thranx, and anyone else they could find.
From the works of Michael Moorcock: John Daker, called to an alternate earth to be the champion of humanity against their dreaded foes, the Eldren, discovered that these humans were Absolute Xenophobes, doing their best to exterminate a peaceful culture who had never done one damn thing to deserve it. He defected to the Eldren and tried to defeat humanity and strike a peace...but the humans fought to the death, every last man, woman, and child. For his "crime" against his own species, the Cosmic Balance sentenced Daker to be reincarnated again and again across a million worlds as the Eternal Champion.
The Ekhat in The Course Of Empire are utterly mad creatures, devoted not only to killing all sentients (albeit saving some, temporarily, if they're useful as slaves), but to transforming the entire universe so that all that exists "is" Ekhat in some way.
Inverted in Anne McCaffrey's Decision at Doona, where mankind's "no contact with intelligent aliens ever" policy came about when, upon the first-ever such contact in history, the alien species in question promptly committed mass suicide.
They're not exactly aliens, but the Auditors of Reality from the Discworld series probably count. They regard life, especially sentient life, as a blight on the universe (and a major bookkeeping headache), and want to see it eradicated.
Their hatred of life is such that it even applies to themselves. They aren't technically alive to begin with, but if they show any signs of individuality (such as refering to themselves as "I"), they disintegrate. The "logic" is that if something is an individual, it has an identity. If it has an identity, it is a person. If it is a person, it is alive. If it is alive, it will die someday. And from the point of view of the immortal Auditors, a mortal lifespan is so short that it might as well end instantaneously.
The Molothos in Ryk E. Spoor's Grand Central Arena hate all other sapients, but are forced by the Arena system to interact with them on a non-destructive basis. This does not make them any happier.
Certain eras of the Xeelee Sequence by Stephen Baxter present the rather disquieting specter of humanity acting this way to everything else, essentially out of a deeply psychotic sense of Sibling Rivalry stemming from our second-place status to the Xeelee.
The buggers appear to be this in Ender's Game, though as there is no communication until the end, it can't be confirmed. It turns out they're not this at all. Rather, they simply failed to recognize humans as intelligent life forms on their own. Given that the number of individuals in Formian society is very small, with Queens acting through hundreds or thousands of drones, they consider murder to be unthinkable. When they realized that each human they killed was an individual roughly on the level of a queen, they felt so guilty that they held no hostility towards humanity for wiping them out.
Some of the human characters seem to skirt awfully close to this, although it's hard to tell because of the very legitimate fear that the buggers will invade a third time and finally wipe out humanity, so the 'in-principle' xenophobes don't stand out much from the people who are just afraid of annihilation. The later books in the series cover the subject in greater detail, considering whether differences in biology and mindset will inevitably lead to a conflict where one species must wipe out the other.
The Yevetha from the Black Fleet Crisis trilogy (Star Wars Expanded Universe). They consider all other life to be vermin and their ambassadors scrub themselves clean with painful showers after any contact with other races, and eventually commit genocide against every world in their star cluster not controlled by them.
This later comes back to bite them when the Yuuzhan Vong, warlike conquerors themselves, invade the Yevetha homeworld — and the Yevetha refuse outside help. The Vong drive them almost to extinction.
Despite having not yet even formally ventured into space, the Fenachrone from the Skylark Series have spent several generations planning to conquer the universe and exterminate any sapients they may find. (They're also almost inconceivably overconfident.)
In the Cthulhu Mythos, one has the Yekubians, who slaughtered every other intelligent race in their galaxy before heading towards ours.
Revelation Space has the Inhibitors, a race of post-sentient machines who wipe out any species that attempt to leave their home systems - though they do it to try and retain absolute control of the Milky Way, to shepherd the Milky Way's stars through the Andromeda collision in a few billion years. Their motives have already degraded after only a few hundred million years - the Inhibitors have become much more brutal.
In Poul Anderson's "Among Thieves" the Kolreshites are described as follows: "The Kolreshite mutation did not show on the surface. Physically they were a handsome people, running to white skin and orange hair. It was quite possible for spies to infiltrate them - but to keep up the pretense, spies had to be ready to take part in cannibalism and worse. The mutation was a psychic twist, probably originating in some obscure gene relating to the endocrine system. One might call it extreme xenophobia. It is normal for Homo Sapiens to be somewhat wary of outsiders until he has established their bona fides. It was normal for Homo Kolreshi to HATE all outsiders, from first glimpse to final destruction". The story then goes on to describe how such Absolute Xenophobes could be tricked into being TOO TRUSTING...
Live Action TV
In Doctor Who, the Daleks would like nothing more than to exterminate all non-Dalek life, and even remake the universe itself to serve Dalek purposes alone. They were created by Davros as a means of ending a centuries-long, hopelessly stalemated war between the Kaleds (his people) and the Thals. Davros programmed them to "survive" by any means necessary, having decided, based on the endless war, that the only way for any one species to survive is by completely subjugating all others.
The Daleks hate each other and themselves almost as much as everyone else. They have been known to start civil wars over trivial differences, one commits suicide in the new series when it discovers that it has been tainted with foreign DNA, and a new faction can't stand its own existence because they were created by the emperor using human cells, making them even nuttier than usual. Even the Cult of Skaro, specifically intended by the Daleks to be individuals and consider new ideas, turned on their leader when he favored becoming less "Dalek" in order to ensure the survival of their race.
Probably the most extreme example from the humans is the Last Human, Lady Cassandra. She removed bits of herself that she saw as being similiar to aliens or altered (inbred) humans. In the end, she became just a single sheet of skin with a face. To current era humans, she would be much, much more alien than many of the aliens.
And just to add icing on the cake, it's stated off hand she's transgendered. While absolutely no one holds this against her, it smacks of Irony that someone who wasn't born the sex they are now is so utterly obsessed with body purity.
Sutekh the Destroyer was a Physical God and Sufficiently Advanced Alien with these tendencies. To preclude the possibility that something that could challenge him might evolve, He wanted to erase all life in the universe, down to viruses and bacteria. He started out by trying to exterminate his own race, the survivors of whom ganged up on him and imprisoned him on Earth. The conflict itself was observed by the Egyptians and became part of their mythology.
Rassilon himself is a horrifically successful Absolute Xenophobe himself. He studied and cannibalized Vampires to develop regeneration technology from their autopsies, and then tried to execute genocide on the race. He created a device that seeded life on the galaxy - life based on the Time Lords' own biodata, and killed everything that did not evolve from said technology. He imprisoned countless Divergents out of the universe so they could never, ever, rise to the challenge of rising against the Time Lords. His crowning act of monstrosity and xenophobia, however, was the Final Sanction, an X-4 or X-5 Class Apocalypse How which would obliterate all of Creation so the Time Lords would Ascend to a Higher Plane of Existence, while leaving the remains vulnerable to the depredations of the abominations of the Last Great Time War.
The Peacekeepers in Farscape are initially presumed to be this: however, though they are extremely xenophobic - particularly around new species - and opposed to hybrids on general priciple, they aren't really true examples of this trope in that they are more interested in conquest than genocide. However, even their usual reputation for xenophobia is largely due to regulations that not all Peacekeepers pay attention to: quite a few frontier officers and captains have been seen flirting with alien females, and some aliens and hybrids (like Scorpius) have managed to attain high office in Peacekeeper command.
The Scarrans however, at least according to Scorpius (who, though biased, has shown a strong understanding of Scarran nature), play this trope straight. This is best summed up in this quote:
"They plan to exterminate the Sebaceans, but they won't stop there! Nor with Luxans, Delvians, Baniks, or a thousand other lower life-forms. They'll stop - when they're the only sentient species left. And if they discover wormhole technology before we do - the galaxy is theirs. And eventually, John, they will find Earth. Your race is defenseless. They'll be raped and slaughtered unless you help us!"
This is the attitude of some of the demons in Angel. The Scourge is the best example; they would like nothing more than to purge the world of humans,vampires and impure demons. They fail to see that they likely have human blood in them as well...
The K'kree in Traveller are limited Xenophobes: they're on a genocidal crusade to wipe the galaxy clean of all carnivorous organisms. No matter whether or not said organisms pose any threat to the K'kree at all, or are even capable of metabolizing K'kree flesh, or even if they're vital to the ecosystems of worlds the K'kree have colonized: meat-eating is EVIL and must be ended at all costs. Omnivores get a pass if they're willing to go vegan; obligate carnivores are out of luck.
During the K'kree-Hiver war the Hivers introduced meat sauce to a few K'kree colonies, they were so horrified that they sterilized the planets in question.
Several factions of Warhammer 40,000. Most notably, the Imperium of Man generally maintains an official policy of Absolute Xenophobia, but it's far from 100% honored, and there are valid reasons for it not being honored, such as that some aliens are harmless and destroying them would be a waste of resources, or that they're actually useful if kept at a "safe distance". Rogue Traders are also explicitly exempt from the usual restrictions on contact with Xenos, and are allowed to trade and interact with them as long as it is done in the interest of the Imperium. (But the average human being is taught to just fight/fear them). The Necrons, for their part, kill all lifeforms, not even limiting themselves to sentient ones.
The Necrons aren't so bad. Sometimes, they just use weird tortures and spread terror, or set themselves up as gods. The C'tan do have a sense of fun.
Well, the Void Dragon and the Deceiver anyway, the other two are crazy.
The Ciaphas Cain novels, specifically For the Emperor!, examine this in more detail. The Imperium and the Tau do not like each other, but are not continuously at war. Cain actually allies with a Tau squad when their interests align, but they split up as soon as it's convenient.
This is also due to him being practical. After all, wouldn't you prefer those plasma guns and rail rifles to be pointed at the genestealers, rather than you?
The Army of the Expeditionary Force in 3:16 Carnage Amongst the Stars seeks to destroy all non-terran life in the universe. This includes non-sentient life.
In case that's not blunt enough, let's be clear that their policy makes the Imperium of Man look like it cherishes and respects all life by comparison. Let's give an example of space gerbils just sort of harmlessly gerbiling around on their homeworld. Faced with this, the top ranks of the Imperium of Man would decide that these could never conceivably be enough of a threat to justify the resources it would take to destroy them, maybe even look into domesticating them. The top ranks of the Army of the Expeditionary Force would decide that they could never conceivably be enough of a threat to justify blowing up their entire star system, and they should be genocided the old fashioned way.
Daemons in Pathfinder, though it's more about wanting to end all life than racial purity. The only reason they don't slaughter each other (much) is because they're all working toward the same end; once all other life in creation is gone, they'll most likely commit racial suicide.
The 2nd and 3rd editions Dungeons & Dragons had the beholders, who were so paranoid and xenophobic that each individual thought that it was the perfect manifestation of ideal beholderhood, and all other beholders were inferior fakes. When a beholder gives birth, it picks out the young that look most like itself, and kills all the others.
Fredrik Pohl's Gateway had the lovingly dubbed Assassins, a xenophobic race which is bent on the destruction of every other sentient being in the universe. Once their equipment is activated by sufficiently advanced races (in this case, the humans), they send a signal to the Assassins to come clean up the mess. Thankfully, the player manages to avoid the destruction of the human race in both games with the help of the Heechee race.
In The Ur-Quan Masters, the titular Ur-Quan are divided into two factions: Kohr-Ah and Kzer-Za. The Kohr-Ah want to wipe out all other sentient life in the universe. The Kzer-Za will settle for enslaving or confining all other sentient life in the universe. Similar to the Ryall, it comes down to a species-wide Freudian Excuse - eons ago, they were all enslaved by a race of evil creatures with mind-control powers, and after finally casting off their shackles (in a thoroughly horrible way, at that - turns out, the evil aliens couldn't maintain control of a being in absolute agony), they decided that they couldn't risk it happening again. So they went to war with all other sentient life. The intervening generations have not mitigated their trauma - Genetic Memory means that it effectively happened to all of them.
In the first Galactic Civilizations 2 expansion, the Drengin undergo a similar (and reference-riffic) split: Their largest and most powerful clan, called the Korath clan, decided to exterminate all non-Drengin life, while the rest of the Drengin simply wanted to enslave the galaxy.
The Ascalonians of Guild Wars. Whose attitudes were that charr were strange and must be culled, and then that the other human nations were weird and must be culled. Anything or anyone that wasn't from Ascalon needed to die. They did love their cleansing.
The Glomdoring Commune of Lusternia subscribe to this notion. It's their ultimate goal to seed the Glomdoring throughout the rest of the known world, while forcibly converting the other civilizations to their own viewpoint as they do. Resistance results in death.
The Shivans of Freespace...may or may not fall under this. They do kill anything that isn't Shivan on sight, but they tend to ignore planets unless they are populated by a space-faring species they're exterminating at the time, and certain unexplained actions they take near the end of the second game have cast considerable doubt on their motives.
The Zuul from Sword of the Stars believe in a divine purpose for their race, which is to enslave and kill off every other species but their own and their "master's". Word Of God says this is partially due to culture and partially built-in instinct; the Zuul were bred by a race of Abusive Precursors as a living bio-weapon to exterminate other civilizations. In-game, making NAPs and alliances with Zuul is all but impossible: Their default state towards everyone is war.
Falmer from The Elder Scrolls series are a fantasy variant; being betrayed and enslaved by their cousins the dwarves instilled into them a hatred of all civilized races, and rebelling against their masters caused them to develop a fondness for war.
Star Ruler's Galactic Armory mod adds the "Inhibitor" AI type. Inhibitors will go to war as soon as possible with any race they detect (after trying to extort them for resources, that is), and rely on weapons that distort space-time. Galactic Armory also beefs up the Remnants - who are long dead, but still have very much active AI controlled ships - rather than just sitting inside their long-dead systems, the Remnants will periodically send out ships to cull the lesser races - and they do a good job of it too, since they start out several orders of magnitude more advanced than the player(s) or computer-controlled empires.
The dark-matter Pa'anuri. They have one name for baryonic-matter entities (which would include us, Earth, our Sun, and all observable (to us) matter in the universe), which is "ANNOYING". Using teraports (since they create gravitic tunnels in space; sort of like having a blind man drilling holes through your house) angers them, and if a species develops to the point of being able to teraport, they blow up that species'es sun. After drawing an extremely costly war against the Gatekeepers, the Pa'anuri moved shop to the Andromeda galaxy, where they began routinely destroying any civilization that invented the radio. The first baryonic space-farers from the Milky Way who went there found several radio shells... All of which are thirty years wide, and then scrambled by a supernova shell. By Earth standards, we would barely have invented the tank by the time our sun would have been blown up.
The Kvrk-Chk of Quentyn Quinn, Space Ranger have two categories of lifeform: "Other Kvrk-Chk" and "food". With these two categories forming a VERY disturbing Venn diagram....
Part of this comes from their world being an EXTREMELY hostile environment, where most non-Kvrk-Chk species would die instantly just from atmospheric pressure or the toxic atmosphere, or the wide variety of scavengers and predators. Due to how hostile and aggressive their environment is, they have to eat their food alive just so the scavengers and decomposers of their world don't rot their food before it reaches their mouth. As part of their culture, a visiting Kvrk-Chk offers the master of the house one of it's own severed limbs as food. Oh, and they consider "Awake and Screaming" a flavor, and sentient lifeforms "chatty food".
The ancient race the Malevol already wiped out all other life in their home galaxy of Andromeda simply because they didn't want to live with them, and came into our galaxy thousands of years ago looking to do the same. Fortunately we had our own elder race with the will and power to oppose them...
The Global Guardians PBEM Universe features the Kalish'chahine, a horrifically warlike alien race who view all other forms of life as food resources. They breed so quickly that they exceeded their home planets' capacity to keep the population fed, and are capable of digesting any carbon-based life. To them, Earth is a smorgasbord waiting to happen.
The Brain Spawn in Futurama wish to wipe out all conscious thought from the universe because "the thoughts of others screech at them like the forced laughs of a thousand art house patrons." Later, their plan is to collect all knowledge in the universe and then destroy it to keep any new knowledge from appearing.
The Traash species in Adventures Of The Galaxy Rangers, Big Creepy Crawlies with the usual tropes that apply, were so xenophobic that "in Traash space, there exists no other lifeform but the Traash." When the Rangers' telepath was able to communicate with them, it was discovered that they hadn't even considered the idea that another species would try to make peace instead of attacking.
Fanon of Invader Zim often depict the Irkens as this, based on the canonical facts that they wish to take over the galaxy and enslave and/or destroy all other species. In-series, however, only Zim himself seems to have this direct hatred of other species - the other Irkens seem to be merely acting out of a desire for power and a sense of superiority.
In most incarnations of Transformers, Decepticons hate anyone who isn't a Decepticon, or anything that is organic in nature.
In Season 1 of Ben 10 Alien Force, the Highbreed were this. Obsessed with genetic purity, they inbred themselves to the point of sterility, dooming themselves to extinction within a generation. They were the first sentient species to develop in the Universe, and they were disgusted with the prospect of younger (and thus "inferior") species living on without them, so they planned to exterminate all lifeforms in the Universe.