Even if aliens did theoretically exist, in settings where the population is confined to a single star system and there is no FTL, neither humanity nor the aliens would be in any position to encounter the other.
Theoretically, intelligence could be a rare evolutionary fluke, rare at least elsewhere in the Milky Way. Even if intelligence evolves on other planets, it may be extinct by the time humans leave the Solar System, or alternatively, humanity could be extinct by the time aliens leave their home system. Thus, even interstellar civilizations may be separated by immense distances or timescales, and unlikely to interact.
Nobody talks about it much, but the existence of other intelligent species would raise uncomfortable questions about whether or not humans are "the chosen species of God." On the other hand, the Catholic church is open to the idea.
The focus of the Sci-Fi in question is political struggle between human populations, and aliens could either help them resolve their differences or serve as a threat encouraging them to do so themselves.
Cowboy Bebop: There was passing reference to life on Ganymede, but nothing intelligent, and it may have only been there after terraforming. Those sea rats are damn tasty. Or at least the people that sell it as some sort of a delicacy say so (Jet says otherwise).
And the freaky monster thing from 'Toys in theAttic' does not count. It's a mutant. Mutant. And possibly a dream.
The "aliens" in Crest of the Stars, known as the Abh, are really genetically-engineered humans.
Armored Trooper VOTOMS is a hard scifi mecha series which deals exclusively with a human based conflict between two space nations.
Kiddy Grade, set within one galaxy, and not only no sentient species, no other life at all has been found so far.
There might not be any aliens in Van Dread, but that doesn't stop Dita from trying to find them. It's also played with; the people of Ma-Ger and Tarak consider each other to be hostile aliens, even though they're really just male and female humans trying their damndest to be One Gender Races through gene manipulation.
One of the things which initially made Mobile Suit Gundam stand out from the pack of sci-fi mech series of its day was the total lack of space aliens. This was primarily done because the writers felt that having alien villains would make them too hard to relate to; they wanted the show's central conflict to be one in which both factions had understandable motives. Other Gundam series have carried on this tradition, with all the major conflicts being between humans. Mobile Suit Gundam SEED has some fossilized remains of Space Whales, but that's about it. It helps that every Gundam series to date has been entirely confined to Earth's solar system, and indeed none of have ever included travel further out than Jupiter.
Played with Gundam AGE, with the UE calling humans "Earthlings," and Federation characters speculating that they are aliens for the first third of the show... until The Reveal that they're the descendants of a Mars colonization project that was abandoned when disease struck.
The Dark Crystal: Inverted. No humans on Thra, although there are multiple humanoids.
Forbidden Planet: The Krell, the ancient race that once inhabited the planet, have been extinct for millennia. Only their technology remains. Which, it turns out, ain't a good thing.
2001: A Space Odyssey may, or may not, contain aliens; the beings who set up the monoliths, receive Dave Bowman in the pseudo-hotel room and are heard only as high-pitched, rapid chittering noises may, or may not be evolved humans. The "Star Child" is presumably the hyper-evolved Bowman, but how this transformation takes place is not specified.
Amongst other things in Dark Star, the characters display absolutely no interest in their computer calculating a miniscule chance of intelligent life in a nearby system, with the implication that previous pursuits of such readings had brought disappointing results. The only alien we see resembles a beach ball with webbed feat which even the guy who brought it aboard has gotten extremely fed up with, and that ends up being only a small (though memorable) part of the overall film.
Additionally explained in Asimov's oft-forgotten early novel, The End of Eternity, which connects to many of his other stories including Foundation, and has as a main plot twist the revelation that if the human race doesn't grow up in the next 10 million years or so and take over outer space, other species will apparently evolve sufficiently to take over all the good planets, leaving mankind stuck on Earth to wither and die out.
However, Foundation and Earth, the last Foundation novel which was written years later (and not long before Asimov's death in 1992), brings up the rather good question of, regardless of their apparent absence here, whether or not species from galaxies other than the Milky Way might perhaps not only exist, but be a potential threat if humanity doesn't band together enough - which is the reason, albeit only subconsciously realized, that the protagonist chose the "Gaia"-style path for humanity. Further, Foundation and Earth also brings up the point that genetically engineered humans who have been so radically changed from baseline humanity could sufficiently meet the requirements of being called "aliens" i.e. the Solarians.
In the Second Foundation Trilogy (written by Bear, Benford, and Brin), it's tangentially revealed that Asimovian robots (designed to protect humans, and only humans) are responsible for the situation, having been required by their programming to carry out innumerable genocides, since the aliens might have been a threat.
Manifold: Space does have aliens, but recurring natural disasters on a galactic scale keep wiping them out before they can meet.
Lois McMaster Bujold's Vorkosigan Saga is a roughly 30th-century Milky Way with no sentient aliens to speak of (though there are alien plants and animals); however, after nine or ten centuries of diaspora, many of which involved various genetic engineering concepts, humanity has undergone speciation to the point that "the aliens [are] us."
Similarly, the Vatta's War series be Elizabeth Moon has humanity spread out to such an extent that Earth isn't even mentioned. Humanity is still the same species, but there is a fair amount of augmentation, both organic and technological, being done and baseline improvements are made to genetic code.
In Frank Herbert's Dune series alien plants and animals exist (including the iconic sandworms), but nothing sentient. Rather, the closest to "aliens" are genetically modified humans and animals. These creatures take a variety of shapes, some almost unrecognizable.
The CoDominium universe by Jerry Pournelle. In the Falkenberg Legions the series features no intelligent aliens. In fact, the CoDominium series is largely lacking aliens until The Mote in God's Eye, which is set far into the future of the series and makes First Contact.
Author David Brin has argued that the galaxy is so large, and the history of the galaxy is so long, that its actually likely that only one sentient species arises in the galaxy at a time. They live for a few million years, then die out, and as they are dying out, the next species is arising on some far-distant planet. Brin's other treatments of this idea range from exultant (Crystal Spheres) to mild fearsome (Lungfish).
This also turns out to be the case in Existence, while the artifact contains the uploaded personalities of dozens of alien emissaries, their species are now extinct.
Robert J Sawyer's Quintaglio Ascension trilogy : Although there are several planets with intelligent life, there is no life in the universe that can't have its origin traced back to Earth - at least not in this iteration of reality.
Technically averted, but played straight in spirit within Honor Harrington: There are sapient aliens (twelve known species), but humanity has settled many thousands of planets without encountering any aliens capable of building spaceships or other modern technology. There is a short story featuring archaeological evidence of an ancient interstellar alien civilization, but they long since died out.
Sort of happens in K. A. Applegate's Remnants series: there are aliens, the Shipwrights, and three other species, at least two of which the Shipwrights created. However, these three species are apparently exterminated by the Troika, and it is implied the Shipwrights may be dying too. The penultimate book involves Tate, Amelia and Yago spending the rest of their lives looking for some other form of life but never finding anything more than bugs.
Everything in Dan Simmons' Hyperion Cantos is more or less a result of human works. Slightly averted as the books sometimes mention aliens, even intelligent ones, although all of those have been driven to extinction or were simply wiped out by humanity. More aversion in the sequel-series Endymion as the main character encounters a few of the said-to-be-extinct intelligent species multiple times, on unknown planets and on a living Dyson Sphere constructed by 'alien' humans.
Played straight initially, then subverted with a vengeance, in The Stainless Steel Rat series. Aliens are completely absent throughout the galaxy up until one book where every kind of grotesque alien monster pops up out of the woodwork. They were just hiding all that time. Seriously.
Played with in The Stainless Steel Rat Sings the Blues, where Slippery Jim Di Griz, the eponymous Stainless Steel Rat, is send undercover to find the first recorded alien artifact. Turns out that it was an artifact left by human time travellers from the future.
In Embedded, humanity has colonized hundreds of worlds but found no sign of intelligent alien life anywhere. Until they get to Eighty-Six....
Zig-zagged in The Golden Age by John C. Wright. Biological engineering has reached the point where (formerly) human beings are able to turn themselves into what amounts to Starfish Aliens as compared to "traditional" humans (amorphous blobs, HiveMinds, a sub-culture of living biologicalSquick, and sentient ecosystems, to name a few) but no humans have ever encountered actual extraterrestrial life and have given up looking, until something from the outside starts to cause trouble for the main character which ultimately turns out to be the evolved cybernetic remnants of a human spacecraft that had been sent out thousands of years earlier, when humanity was still interested in exploring space.
Subverted a lot in the Revelation Space series by Alastair Reynolds. There is various odd alien fauna and flora, but there are no living alien races comparable in intelligence to humans. However, human archaeologists continue to find the remains of several highly advanced civilizations all the time. More worrying is the fact that they all seemingly became extinct shortly after they discovered interstellar flight and started exploring deeper space. There turns out to be a reason for that - and the author uses it to cleverly explain why the Fermi paradox seems to be in effect in the first place. The Fermi paradox itself is the driving mystery behind the events of the series.
The In Death series. There is space travel in Robb's 21st century, but it's mostly background, and there's no mention of non-human life. (Aside from the monsters Eve chases)
Last Legionary: Although there are a wide variety of humanoid forms; they're all genetically human, just mutated by the effects of their respective environments. High-gravity worlds get shorter, heavier humans and so on. The only genuine alien is Glr, and her species isn't from the same galaxy.
There are many planets in The Diving Universe, but they're all populated by humans. Not even the nomadic Fleet, in all its travel across known space, ever found an alien intelligence.
In the Matador Series humanity has colonized most of the galaxy's Earthlike planets and found nothing sapient. There is a race of precursors called the Zonn that left interesting ruins on multiple worlds, but they've been gone for tens of thousands of years.
In the Cassandra Kresnov series by Joel Shepherd, other sentient species besides humans do exist, but they are barely mentioned in the story and have no bearing on the plot, which mainly concerns politics within the human Federation, and between the Federation and the other human faction, the smaller and more technologically progressive League.
Glen Cook's Black Company novels provide a fantasy version. The first three books take place in a Standard Fantasy Setting, except that the entire series is populated solely by humans. The only exception is the Plane of Fear, where a handful of nonhuman beings are intelligent, but none of them have anything resembling a culture or civilization.
In Mikhail Akhmanov and Christopher Nicholas Gilmore's Captain French, or the Quest for Paradise, by the 22nd millennium, humanity has colonized thousands of worlds and scouted out tens of thousands of more in three spiral arms of the galaxy. While many of the settled planets have their own flora and fauna, no intelligent alien beings have been discovered. The only non-humans (besides those who have genetically-altered themselves) are a Servant Race created on one planet. They later rebel, and the resulting war devastates the planet.
Initially played straight in Andrei Livadny's The History of the Galaxy series, as humanity is expanding and colonizing hundreds of star systems. Subverted about halfway through when three alien races are discovered in short order and remains of a fourth. More are discovered later.
The Lost Fleet series takes place some time in the 27th century, with humanity spread across hundreds of star systems and no sentient aliens in sight... up until about halfway through the first series, at least. Turns out that there are at least three, two of them decidedly unfriendly.
The Quantum Thief-trilogy takes place entirely within the Solar System and no true aliens are to be seen, although Transhuman Aliens come in all shapes and sizes. In the final novel, The Causal Angel, the issue is brought up. Though not outright stated, it's implied that any sapient life that doesn't destroy itself will learn how to break the Planc Locks and create a new, perfect universe for themselves to inhabit.
The 2000s Battlestar Galactica has no aliens: just robots, clones, and the occasional 'angel'. However, humans evolved independently on at least two different planets. Then again, Colonials could more accurately be described as Near-Human aliens who are somehow biologically compatible with both Humanoid Cylons and Our-Earth's early Human species, since we're meant to be the end result of all three cross breeding in prehistoric times. Finally, there is absolutely some kind of intelligent god-like being served by messengers.
Firefly, ostensibly because humans make more interesting foils for humans. Lampshaded when a "genuine alien" at a sideshow in one episode turns out to be a mutant cow fetus in a jar, with some creepy lighting thrown in for good measure. Word of God confirms the nonexistence of aliens in this particular universe. The fact it is set in a single star system is also a factor.
Inara: Do aliens live among us?
Kaylee: Yep. One of them's a doctor.
The Red Dwarf verse contains no multicellular alien life, and in the novels it's explicitly stated that Earth has been proven to be the only place in the universe where life appeared. In the early seasons this added to the isolation and paranoia of the main characters. Later series introduced other life forms, but most of them are leftovers of human genetic engineering projects, or otherwise artificially created (I.E. robots or holograms) and on a very rare occasion they're descended from some form of Earth creature (the Cat being the best example)
This still didn't stop them from poking fun at it though. A running gag in the first two seasons involved Rimmer constantly suspecting aliens to have something to do with whatever problem has just befallen the crew, including one instance where he suspected aliens were trying to communicate by breaking Lister and Cat's legs, and then finishing a jigsaw puzzle. Another episode played it for laughs when Rimmer was convinced that a mysterious pod that they recovered contained an alien life form. It was actually just one of Red Dwarf's garbage pods; Lister and Holly knew right away, but went along with Rimmer's idea just for fun, but that didn't stop Rimmer from speculating that his supposed aliens "must have looked something like a roast chicken").
The BattleTech Universe is renowned for its lack of intelligent aliens. The lack of aliens allows its Black and Grey Morality of interstellar politics between human groups to thrive. There are primitive aliens, but they were discovered in a unknown system by a JumpShip misjump (read: they'll never interact with the rest of the universe), and they only appear in one novel, Far Country.
When Anarchy Online was first released, humanity was thought to be it for intelligent life in the galaxy, though the backstory novelProphet Without Honour did include at least one being that was not at all human. The Shadowlands expansion introduces the Xan — a race of Precursors who created humanity, all but destroyed in a terrible cataclysm eons ago. One of the surviving factions (the Redeemed) launched great space-arks that were meant to seed life across the galaxy, but the other faction (the Unredeemed) destroyed every ark except the one that landed on Earth. Alien Invasion wiped that out by revealing the Kyr'Ozch aliens, who invaded Rubi-Ka due to actions taken by the players in the Shadowlands expansion — except a quest added to the game after Alien Invasion's release revealed that the Kyr'Ozch were created and are being controlled by a god-like being as old as the Xan who survived the cataclysm.
In the Killzone games, it's 2360, humans have colonized dozens of worlds, but haven't found any alien lifeforms whatsoever. The conflict itself is between humans and altered humans.
This trope is played to the letter (to great effect) in Starlancer, which is ostensibly a retelling of World War II IN SPACE.
And then averted in Freelancer, the spiritual sequel. However played straight partialy because even that main bad guys are actualy aliens the most of alien presence in game are thousands years old artifacts. Setting of the game are humans colonies and whole plot is driven by human characters, although sometimes possesed by alien. Plot is more alien conspiracy than alien invasion and general setting of the game is playing straight this trope, only with exception of those artifacts.
Xenosaga: despite a significant portion of the galaxy being colonized, there are no real aliens. The apparently alien Gnosis are actually altered humans and supernatural beings such as U-DO and chaos were created or at least given their present form by humanity's collective will.
The alien planet Xenogears takes place on, meanwhile, has some native life but didn't have any intelligent lifeforms before the human colony ship Eldridge crashed there.
Imperium Nova has this by default, but some players choose to role-play their houses as aliens and, in one case, a game administrator orchestrated an alien invasion of a galaxy.
In Infinity: The Quest for Earth, there are several hundred worlds grouped in clusters in several parts of the galaxy, and no other races have appeared; according to the developers, this is mostly to avoid what they think is the overused idea of a plethora of races.
In Dead Space, humanity has no qualms about cracking apart planets (and thereby destroying entire solar systems) for resources, since there are no aliens around to protest. At least until the game begins, and that's a bit of a cop out, since although the original Marker may have been created by aliens, the one in the game is a reverse-engineered human copy. And the Necromorphs aren't aliens, they're reanimated human corpses.
Justified in Dead Space 3, Intelligent alien life did happen to exist and was rather abundant at some point millions of years ago, but they—like humanity, fell prey to the Marker's influence and were all wiped out by the Brethren Moons created through Convergence events. Leaving the galaxy in a state of 'dead space' and humanity alone in the galaxy.
Elite 2: Frontier has flying saucers in secret military bases, but the game play plays this trope perfectly straight because the only inhabitants of the whole galaxy are humans. However, the sequel (Frontier: First Encounters)) averts this and reintroduces the Thargoids (they first appeared in the original, elite, as a random encounter) , an actual alien race which inhabits the systems of Polaris, Pleione and Miackce. The player's experiences with the Thargoids are the "first encounters" referred in the subtitle.
In some Super Robot Wars timelines, all the Human Aliens are actually descendants of a lost civilization from Earth. Even the Einsts have some connection to Earth, though they mostly hang out in a parallel universe.
In the MMO EVE Online there are five distinct sentient races (only four are playable) and several non-playable races within the game, however they are all descendants of Human beings who traveled through a wormhole in to the space of New Eden 25,000 years before. Even newer races introduced such as the Sleepers are believed to be of human origin. The only non-human life are flora and fauna.
The central conflict in the multiplayer shooter Titanfall is between two human groups.
In Total Annihilation, the Galaxy has already been thoroughly explored and colonized by humanity thousands of years ago, and no hints of intelligent alien life are mentioned in the backstory (though there are alien plants on some of the planets battles are fought on). Both Core and Arm factions are derived from Earth human stock.
Like-wise with Spiritual SuccessorPlanetary Annihilation which follows an endless war waged by the machines of man long after we've shuffled off this mortal coil. There are plants on some worlds but no higher lifeforms.
Outpost 2 is also an Absent Aliens setting, with only humans that are trying to survive after earth is rendered unlivable by meteorites. The conflict comes between two factions fighting over the scant resources and trying to win an evacuation race from New Terra, which is being destroyed by a terraforming project by one of the factions gone wrong.
Section 8: Prejudice presents a plausible explanation for the complete absence of any alien lifeforms in the galaxy, despite humanity having spread out and colonized a huge chunk of it. Long before the game, the Earth government secretly sent out an advance wave of super soldiers, whose mission was to move from planet to planet committing genocide on all potential competing lifeforms in order to pave the way for human colonization of the galaxy. And it worked.
However, after the colonization was complete, the government attempted to wipe out the super soldiers using a huge army of conventional special forces. The special forces are implied to have been curbstomped by the super soldiers, who then disappeared for years. Then they came back with an army of rebels and attempted to take revenge by committing genocide against the humans, but were ultimately defeated by the government forces, including the player.
Depending on the game, subverted, averted, or turned into a pretzel in Escape Velocity, since each game in the trilogy takes place in a new universe.
Lord-knows-what-to-call-it in EV Nova. The Wraith north of Polaris space are insular, space-living Starfish Aliens that only have a role in one storyline, and a minor one at that, so they're effectively Absent Aliens plotwise. Double Subverted with the Krypt, which are the result of the Vell-os ruling council having imbued their minds into their nanites in the backstory. This makes them human offshoots instead of actual aliens.
Capcom's Lost Planet series likewise features a conflict primarily between the NEVEC corporation and various factions of Snow Pirates. The Akrid are dangerous lifeforms native to E.D.N. III, but they're non space fairing and non sentient.
Mass Effect plays with this and Invisible Aliens as a major plot point. The disparity between the half-dozen species that do exist and the sheer abundance of extinct civilisations, shows that while the galaxy regularly produces intelligent life, they tend to die off rather abruptly. It turns out there is a very good reason for that, in the form of race of sentient starships who arrive to wipe out all advanced civilisations every 50,000 years.
Also forms part of the backstory of humanity. While humans knew they weren't alone since discovering Prothean ruins on Mars and the Mass Relay masquerading as Pluto's moon Charon, it took them over a decade of exploring various systems and opening new relays before they finally ran into the Turians, introducing them to the galaxy at large.
RayStorm sees Earth advancing in space travel enough to set up a series of human-inhabited colonies in a distant star system, known as the Star Federation. The plot sees the Star Federation attempting a revolution against Earth, with a squad of fighters fighting for Earth as the protagonists.
In Fine Structure, Humans are demonstratively the only intelligent species in the entire universe, because 3+1 dimensions (our universe) is apparently an extremophile environment. There was one other intelligent species, but it was destroyed (presumably) billions of years ago.
The BattleTech animated series has alien life but no intelligent nonhuman beings. See the Tabletop Game entry for more details.