The Golden Tribe of Heroic Age. They were reputed to be able to create planets and predict the future (though whether these tasks required the use of machines or not is never explained), and are treated as gods by the Silver Tribe.
The enemies of a Mazinger Z spin-off (Z Mazinger) were aliens so powerful and so technologically advanced they were mistaken by gods in the past.
In Neon Genesis Evangelion, the giant monsters attacking Tokyo-3 are called Angels and seem akin to gods, but are actually (according to one of the supplementary sources) expressions of one of a pair of competing "Seeds of Life" launched eons ago by unknown Precursors. What Shinji does at the end also seems to lean towards religion, although it may be interpreted as just science, putting the right objects in the right place and having the desired reaction.
Aforementioned supplementary sources also imply that the Secret Dead Sea Scrolls everyone based their actions around is actually Lilith's partially-translated instruction manualSEELEmistook for a religious text. That's right: billions died because of a misunderstanding. Poor Communication Kills taken to the extreme.
It turns out that this is the backstory of Kyuubey from Puella Magi Madoka Magica. Kyuubey is otherwise a Magical Girl mascot character, and is capable of teleportation, telepathy, some form of Invisible to Normalsnote it's unclear if it's actually tied to magical potential, or if Kyuubey just doesn't want to be seen by them, and turning people into Magical Girls, among other things.
Nagato Yuki of Suzumiya Haruhi is a prime example of this. By chanting computer code, she can manipulate matter and space with great precision and scope.
Yuki also has a superior, the mysterious Kimidori Emiri, and two Evil Counterparts: Asakura Ryouko, a superpowered, really, really freaking scaryUncanny Valley Girlwho tries to kill Kyon without even losing her cool and nice attitude, and Kuyou Suou, an Emotionless Girl whose alien race is at war with Yuki's.
Also includes a bit of a Starfish Aliens touch, in that they had to create humans in order to try to understand them (the "alien" characters would be more accurately described as artificial humans) and are rather interested in the fact that mere matter can apparently have intelligence.
In Tenchi Muyo! the Juraian royalty are semi-divine Sufficiently Advanced Aliens through the pact struck with Tsunami, one of their universe's three Physical Gods (before that they were and still are just Space Pirates). The Word of God also has it that their universe has a real, transcendental God who created said Physical God and her two Sisters, and that this God's avatar is Tenchi.
The Anti-Spirals of Tengen Toppa Gurren Lagann. They live "in the space between the tenth and eleventh dimensions", can accurately count the exact number of people living on a given planet instantly, hide the moon in a dimensional pocket, and insert genetic programming into individuals of other races to use them as messengers. Furthermore, they can create virtual spaces in which they control all the laws of physics, even directly modifying the probabilities of events occurring, and they can trap their opponents within these spaces. To say nothing of their cruder abilities: physically tossing entire galaxies as weapons.
The Earthlings from Vandread. They grow humans like crops, have giant, self sustaining battleships, can copy the shape and powers of the Vandreads, and live by replacing their body parts with the body parts of the aforementioned humans. Their Enfante Terrible leader can communicate telepathically and crush things/people with telekinetic powers.
Gantz, after running though a whole gamut of alien types, seems to have this trope as its conclusion.
Haiyore! Nyarko-san takes the ideas about H.P. Lovecraft (see Literature below) and runs with them, outright stating that the Cthulhu Mythos is based off of stories told to Lovecraft by aliens. By extension, the gods of the Mythos were inspired by members of alien races; the title character, Nyarko, is a Nyarlathotepian, but it's unclear if she's the Nyarlathotep or if it's just a nickname.
Runners-up would be the Watchers and the Celestials, who hate each other's guts, interestingly.
The Watchers believe it's best not to interfere with the development of other worlds and races (the actions of Uatu, The Watcher that frequently bends these rules, notwithstanding). The Celestials (pictured above) are all about interfering — they guide the evolution of planets and destroy those that don't satisfy their standards. It's not a surprise that these two don't get along — not that it really bothers the Celestials, since the Watchers' actions against them are limited to disapproving stares.
Recently Jonathan Hickman's Avengers and New Avengers series have introduced multiple races of seemingly god-like aliens that inhabit the multiverse. Most of these races in fact inhabit and regularly travel between multiple realities, conquering (or destroying) not just planets but entire universes. The Builders, an advanced race that took all the galactic powers of Earth-616 (the primary setting of Marvel comics) to barely defeat, are laughed off by an inter-dimensional traveler as "only" having influence in several thousand realities. Several more far more dangerous races such as the Black Priests, Ivory Kings, and Map Makers have since been introduced.
In the Earth X trilogy (Earth X, Universe X, Paradise X), all the gods are sufficiently advanced aliens (evolution wise), it's a long story.
Shag and Varx in With Strings Attached are of some “lizardy, birdy” race with technology sufficiently advanced to shuffle people from one dimension to another for an undergraduate class project, to bestow people with considerable power, and to maneuver those people into annoying situations. Jeft, who is a Grey, pretends he's a god, but the others are quick to distance themselves from that definition.
In Child Of The Storm, Kryptonians were this, with their powers under a yellow sun (though Word of God has hinted that the vast majority were 'only' at Asgardian level - which still means that each is a Person of Mass Destruction / One-Man Army - on the grounds that the planet would not otherwise have survived its 'Age of Wars'), and their literally godlike technology, which made them the only equals of the Asgardians, despite being mortal.
In Contact, a central theme is science versus religion. The main character is an atheist who looks down on her lover's blind faith, and in the end she is the one who has an essentially religious experience with an advanced alien that everyone else can only take on faith. Makes you wonder, if there really is a God, is he perhaps just a really advanced alien?
In John Carpenter's Prince of Darkness it is revealed that the Church has hidden the truth for 2,000 years — that Jesus was an alien.
Jeff Bridges's species in Starman might count — there seems to be nothing his magic balls couldn't do.
In the Star Wars Expanded Universe, there were the Celestials, a race of even more mysterious beings who used impossibly advanced technology to shape entire star systems, and may very well have been connected to the physical embodiments of the Force itself.
The fellow MCU film Guardians of the Galaxy introduces Celestials, mentioned in the Comic Book section and pictured above. There is even a cameo of Eson the Searcher, obliterating a failed experiment.
The Station aliens from Bill and Ted's Bogus Journey, who are identified by God Himself as the smartest beings in the universe. In less than an hour, they raid a hardware store, then casually build two robot duplicates who proceed to utterly demolish two other advanced robot killers from the future.
The Great Houses from the Faction Paradox continuity. They anchored the relationship between cause and effect whilst the universe was still in its infancy, and their home planet acts as a mean time for the entire universe. When they go to war, they use entire cultures as weapons.
This is the central conflict of Contact, both the novel and the movie based on it, by Carl Sagan. The main character is an atheist and believes in rational explanations for everything, but at the end her journey to the center of the galaxy is revealed to be in every respect a religious experience.
The book is even more explicit; the journey is to an artificial world where the aliens are researching physical constants looking for messages written into reality itself — a church the size of a planet. And once they return, the main character is able to find one of these messages herself (in pi). Thus, Sufficiently Advanced Science is indistinguishable from religion. Or, rather, Science and Religion reach the same conclusions via different routes.
The Shrike. The thing can travel through time, kill all of its enemies in a blink (by freezing time around them) and impale them in a metal tree designed to torture them for centuries.
The TechnoCore: They created an exact replica of the Earth. Later it's revealed that the Earth was actually teleported instead of being swallowed by the black hole on its core. Also, they created the Death Rods, the Farcasting system, and a device to give immortality to humans: the Cruciform parasite.
The "others" (the ones who actually teleported Earth when the TechnoCore entities were freaking out in fear).
2001, 2010, and their sequels explore this in great detail, starting with the aliens' uplift of proto-humans in the African savannah, and progressing to the modern era when it's discovered that they've seeded the solar system with monoliths designed to alert them when humans start to venture into space. They then deliberately capture one (David Bowman) and forcibly ascend him in order to create an intermediary. In 2010, they turn Jupiter into a star to protect the evolution of life on Europa, and allow HAL to join Bowman. In 3001, the aliens put an unusual twist on the trope; despite their apparently godlike power, they are still bound by the laws of physics, meaning they cannot break the speed of light. This is actually a violation of canon, since 2010 has Bowman describe his awareness of how the c limit can be broken, but Clarke retconned this in turn by denying that any of the other novels was a straightforward sequel of its predecessors.
In the Rendezvous with Rama series by Clarke and Gentry Lee, the unseen beings responsible for the construction of Rama and its sister vessels are compared to God by the characters; this point is driven home rather anviliciously in the final novel.
The idea of the Christian God being a Sufficiently Advanced Alien appears in probably more SF stories than can be easily enumerated, but this verges more upon the territory covered by Ancient Astronauts.
Most of H.P. Lovecraft's aliens fall into this category: Cthulhu and his ilk do not even have hidden technology. They just are. In fact, Lovecraftian characters' tendency to consider the aliens gods extends to the fans as well. Ask a general Lovecraft fan, and he will very likely tell you, "Cthulhu is a god."
Lovecraft did write several stories involving gods like Nodens, Bokrug and ones from established mythology like Hypnos and Bast, who conform better to traditional ideas of godhood, but there's a very good reason for that. Since they're all set in Dream Land, they actually aretraditional ideas of godhood.
There are Azathoth and Yog-Sothoth who approach Yahweh in terms of power, even if one is an idiot and the other is locked out of the universe.
Animorphs has two, and manages to justify the All-Powerful Bystander aspect of this trope. The Ellimist seems to be good and aids the Animorphs at several points, but often refuses to explain why or help them as much as he could. Eventually he explains that he has an Evi L Counterpart, Crayak, who seeks to destroy all life just as the Ellimist wants to protect it. A direct fight between the two would destroy themselves and the universe, so they created a "game" where each tries to fulfill their goal within certain agreed-upon rules. So basically, it's the Cold War with god-aliens.
Uriel from Clive Barker's Weaveworld is probably one of these, although it's bought into its own hype and thinks it's an angel.
The title character of Isaac Asimov's "Azazel" series of short stories is either this, or an actual demon — and possibly both. The stories can't seem to make up their mind, which fits in with the Unreliable Narrator who may just be making them all up.
The Humanx Commonwealth series by Alan Dean Foster features a vast array of alien species of varying technology levels, but this particular trope belongs solely to the Xunca. Living a billion years ago, they dominated the entire galaxy and regularly converted entire planets into machines for various projects. They fled to Another Dimension after encountering an unstoppable galaxy-devouring horror, but not before leaving behind a superweapon built out of the Great Attractor, to which the main protagonist, Flinx, is the key. That's galactic-scale engineering for you.
In Design for Great-Day, Alan Dean Foster features humanity (or to be more specific, the Solarian Combine), as a super-advanced multi-species who are on the brink of transcending matter itself and becoming Sufficiently Advanced Aliens.
The Gods (or "Ymirian Guards") in NerhÃ»n are actually highly advanced aliens from the nearby planet Ymir who used EnÃ'r as an experimental location for genetic modification. It got slightly out of hand, though...
The eponymous aliens of S. M. Stirling's The Lords of Creation series alter environments on a planetary scale and create interdimensional gateways with ease.
The eponymous AI of Charles Stross' Eschaton universe has the power to have scooped up a large chunk of humanity and scattered it both across lightyears of space and centuries of time. It's also been known to wipe out entire solar systems that mess with time travel.
His novella Palimpsest is about Stasis, an organization that has reterraformed the Earth multiple times, redesigned the sun, moved the entire solar system outside of the Milky Way and which basically treats time as its bitch.
It's implied in Priest-Kings of Gor that they're motivated largely by intense boredom (Misk has to be physically restrained from committing suicide when the opportunity arises) and that they just think people are interesting.
The Strugatsky Brothers play with this trope on two different occasions. Their main mythos includes a hypothetical (known only through archeological evidence) race called Stranniki ("Wanderers") who are suspected of messing with human civilization in unclear ways. Roadside Picnic is based on the premise that sufficiently advanced aliens visit Earth, leaving a bunch of (again) confusing artifacts.
Palmer Eldritch in The Three Stigmata Of Palmer Eldritch is an example of this trope.
The Leatherfaces in Under the Dome are the children of a sufficiently advanced alien race. They exist outside of normal time and space, don't even seem to remember what corporeal bodies are, and play with humans the same way that human children might "play" with ants using a magnifying glass. Although they do use machinery, an invincible box the size of a Tivo set that can project a five mile high dome capable of stopping a cruise missile is definitely pretty advanced.
The ancient Arisians and Eddorians of the Lensman universe. The Arisians come closest, having direct mental control over matter to a level that the Eddorians do not.
In Larry Niven's Known Space stories, the Outsiders have technology that the other species — even the Puppeteers, who are at least ten thousand years ahead of humanity — cannot even begin to comprehend much less replicate.
The Jenoine of Dragaera. It takes the full attention and utmost efforts of Sethra Lavode, the most powerful sorcerer on the planet due to being a two-hundred-and-fifty-thousand-year-old vampire to kill a single Jenoine scout. They are so powerful that the gods of this world, who are actually former slaves of the Jenoine who rebelled with magic learned from their masters, are scared of them.
In Stanislaw Lem's The Cyberiad, a scientist called Klapaucius theorizes that there must exist a civilization that is on the highest possible level of development. He eventually finds it, but he's shocked to see that they do absolutely nothing. This is because they think doing anything when you're perfect is pointless; "You climb to reach the summit, but once there, discover that all roads lead down!"
Rather common in Perry Rhodan. Perhaps the most iconic type of Sufficiently Advanced Alien in the setting is the "super-intelligence", typically (but not necessarily always — more exotic origins have been described) the collective disembodied minds of one or more entire precursor species making up one distinct entity that usually claims one or more galaxies (with all their 'lesser' inhabitants) as its personal territory. (And yes, our galaxy along with a bunch of others is nominally governed by such a being as well; it's the original source of the protagonists' immortality phlebotinum, for one. Thankfully, IT is usually content to remain a bit more obscure and less actively interventionist than a lot of its colleagues.) At least two more Evolutionary Levels above these are known to exist...
In Peter F. Hamilton's Commonwealth Saga and Void Trilogy, you get the Silfen, who are elves that can travel between planets by walking the Silfen Paths. Even though humans are pretty sure the paths are actually disguised wormholes, they aren't able to understand how they work, or even to detect the paths. In the Void Trilogy some of their "magic" was reverse-engineered by Ozzie Fernandez Isaacs to create the gaïafield, which allow humans equipped with gaïamotes to share emotions and dreams. The Firstlifes who built the void could also qualify, as no one understand its purpose or how it works.
Michael Moorcock's Dancers at the End of Time are reality warping sufficiently advanced humans. They reached godhood one million years before the beginning of the story, which, ironically, caused humanity to fall into decadence by boredom (omnipotence can do that apparently) and by the beginning of the first book, only a few hundreds of them still exist on earth, yet, even diminished as they are, they are still by far the most powerful race in the universe (well, the fact that their technology is so costly in energy that it is dramatically speeding up the heat death of the universe means that there are not that many potential rivals anymore) and are still able to understand their own technology, the problem is that they use it to built pink suns on a whim or tinker with the space-time continuum to pass time instead of trying to fix the mess they created. It is even implied that some of them actually go to other universes and start insanely destructive wars against gods because they have nothing better to do.
Langhorne and the other founders of Safehold are this to the unwitting colonists. Shan-Wei, a founder who resists the idea of setting themselves up as "Archangels" is defeated and becomes the planetary religion's equivalent of Satan.
The Preservers of Paul J. MaCauley's Confluence series are worshiped as gods by the inhabitants of the title construct, a literal space needle several thousand kilometers long which they built and populated with genegeneered species of their creation. Subverted in that in the second book it is revealed that they were actually Suficiently Advanced Humans and that the series takes place millions of years in the future.
The Precursors of David Brin's Uplift series who are directly or indirectly responsible for the existence of all but a tiny fraction of a percentage of intelligent species. That tiny fraction apparently includes us, although there is debate about it that eventually becomes a multi-sided holy war.
The Souls from The Host especially when it comes to medicine, which is almost ridiculously effective, ridding the body of infection, fever, cancer, whatever, pretty much instantly.
The Builders who created the title construct of Eric Brown's Helix, a construct which contains thousands of constructed planets linked together in the titular shape.
Robert Sheckley's short story "Hunting Problem" is about a Sufficiently Advanced Alien who is the worst member of his scout troop and desperately needs to win a merit badge before the upcoming Scouter Jamboree. To this end, he engages in a hilariously inept attempt to obtain a human pelt using "colonial" methods such as shapeshifting and summoning objects out of thin air.
Orion First Encounter: The makers of the Orion. They can rewire people's brain, bend the time/space continuum and make holographic boxing gloves that can interact with whatever they come into contact with.
It seems like Star Trek had dozens of these buggers running around the edges of the Federation: The Cytherians; Trelane, the so-called "Squire of Gothos"; the Organians; the Q; the Thasians, who reared Charlie "Charlie X" Evans; The Companion; Nagilum; the Caretaker; the Douwd (one of whom wiped out an expansionist empire in a fit of anger); Bajor's "Prophets" (even though they never came out of the wormhole); Apollo and the other Olympians; even Quetzalcoatl (in an episode of the animated series). It's implied that Wesley Crusher became one when he was Put on a Bus, as did Kes from Star Trek: Voyager.
The Metrons, from the famous TOS episode where Kirk fought the Gorn.
Also the Guardian of Forever (or alternately, the ancient race that created said Guardian).
Humans can be this to a sufficiently primitive race if first contact is sufficiently bungled as both Picard (in the TNG episode "Who Watches the Watchers?") and Kirk (in Star Trek Into Darkness) discovered.
Babylon 5 has Lorien and the First Ones (the Vorlons and the Shadows can be killed, so they're not on this level; and they represent themselves as angels and demons respectively rather than as gods).
Mystery Science Theater 3000 parodied this trope for everything it was worth in the Sci-Fi era with the Observers, a race of disembodied brains carried around in bowls by bodies that they claimed didn't exist. Despite claims that they were possessed of all knowledge in the universe, they are an omnipotent race of morons — assuming that Tom Servo was one of them because he did well on an IQ test and he started carrying an olive in a dish and pretending it was his brain, and finding chili dogs an incredibly fascinating concept, to name just two instances.
In Stargate SG-1 the Ori fit this: they are immaterial, pretty close to all-knowing, and have near absolute control over natural forces. Their followers point out that there's really a fair argument to be made that the Ori are gods. To which SG-1 usually retorts that even if their power and knowledge are real, their actions make them unworthy of devotion.
In the Stargate Verse, the Ancients, the "good guy" counterpart to the Ori, are also "ascended" human-like beings. Though they have a strict policy of not interfering in mortal matters, the Ancients left all sorts of neat tech lying around when they ascended (including the eponymous stargates and city of Atlantis). The Ancients are often said to have re-created human life across the galaxy when they started ascending.
While the Nox are Space Elves instead of Energy Beings, what little we've seen of them seems to paint them in this light.
In Stargate Universe, when the Destiny comes across a planet that shouldn't be there that looks as if it was built for them, they theorize all-powerful aliens must've built it, especially because of a huge monolith with strange writing. A theory that gains more credence when a group of people left behind on that planet suddenly and inexplicably show up a galaxy away... after freezing to death. Also the "all-powerful aliens" bit is not too outlandish in the Stargate verse, what with the Ascended (it would be well within the power of the Ascended to create a perfectly habitable planet).
Farscape featured these occasionally, and they ranged from the humanoid to the utterlyotherworldly. By far the most extraordinary were the True Ancients, who had power to control minds, open wormholes, and in the case of at least one, "wrap time around his little finger."
In Doctor Who there are the Eternals, for instance, who dismiss the Time Lords with "Are there Lords of such a small domain?" In the Expanded Universe novels, a group of Eternals are the seldom-mentioned gods of Gallifrey. And then it turns out that The Eternals themselves greatly respect creatures known as the Black and White Guardians, who are as far above them as they are above Time Lords.
The Time Lords themselves also count. Having made technology to travel anywhere in time and space, as well as other goodies like the Sonic Screwdriver, and being capable of cheating death.
In Battlestar Galactica (Classic) the Seraphs are this to the Colonists. Interestingly, the Colonists regard the Seraphs as exactly this - technologically advanced aliens.
Later, the Colonists take this role to the Terrans, and to Earth.
Subverted in Earth: Final Conflict; the Taelons view themselves as this out of arrogance, but, as Energy Beings who can't replenish the energy they're made out of and burn, are actually an evolutionary dead end. Their technology appears wondrous, but it, too, dies from lack of sustenance without outside intervention.
In Magic: The Gathering, the mer and kor on the plane of Zendikar each worship a triplet of gods, the legends of which are based on the horrific Eldrazi (Eldritch Abominations). The mer gods Cosi and Ula are based on the Eldrazi monstrosities Kozilek and Ulamog.
Karn the Silver Golem was a sufficiently advanced robot, an assembly of artifacts indistinguishable from an old-style Planeswalker. He even created his own world.
The C'tan of Warhammer 40,000. They fall somewhere between Sufficiently Advanced Aliens and Energy Beings, given that they had no physical form and little power to influence the world until their followers gave them bodies.
The Old Ones were Sufficiently Advanced Aliens long before the C'tan decided to stop ignoring sentient races and start eating them. They seeded worlds with life, created safe realms within the Warp, and created the Eldar (who later ascended to this position themselves) and the Orks.
Eldar were this during their peak. They would move the stars for the view.
Arguably, they still count. Yes, they're slowly dying out as a race and a culture, but they still have some very nice technology left over that can't really by explained by human science. As do the Necrons, the former servants and now jailers of the above mentioned C'tan.
In the 6th Edition of Hero System there are at least three races the Malvans, the Odrugarans and the Mandaarians capable of doing anything from colonizing and terraforming asteroids and planets to shattering planets, pull a moon or planet out of its orbit and “fling” it away from its parent body, transmute one type of matter into another type of matter (thus allowing for the nigh-instantaneous creation of objects from “thin air”, quickly and easily clone any living creature, then copy or transfer memories into the clone, create force-fields that protect against virtually any force (including magic and psionics), cross the Milky Way Galaxy in as little as a day (military starships) or a week (common civilian models, teleport people and objects over interstellar distances (and sometimes further), giving themselves any superpower they desire and cure nearly any disease, heal nearly any injury,and extend lifespans for centuries (or even millennia, or can even live forever. :Luckily they're all peaceful or too lazy from being able to replicate anything they want to be a threat.
If the dialogue from the monolith use means anything, this is probably what the player is in SimEarth.
In MARDEK, every other race, especially the Annunaki. However, they are weak enough that they can be defeated outnumbered and forced into a situation where they are forced to fight out of their element. Moric, the first you fight is a necromancer, and is forced to fight himself, first drained of energy after being interrupted in the middle of casting a massive necromantic spell, and then again in a place where he didn't have any dead to raise. Qualna, the second, had powers mainly based around manipulation, deception, and, if necessary, combat from a great distance away. He never expected to be in a real fight at all.
The Halo Array: 7 (originally 12) ring habitats that act as fortresses and weapons of a kill-all-life-in-the-Galaxy-bigger-than-a-microbe scale. Had the original 12 been activated all at once, the kill-effect would have gone far out into the Local Cluster. The rings themselves have almost the radius of the Earth.
The Ark: C&C for the Halo Array, as well as a Halo-factory and a refuge from the destruction. Positioned 3 galactic diameters out from the Galaxy's core. Scale is... considerably larger than a Halo. Comparison◊.
The Ark itself comes with its own small star that moves around it.
Halo: Silentium further reveals that Installation 00 was known by the Forerunners as "the Lesser Ark". The Greater Ark was even more massive, and it was there that the Forerunners made their last stand against the Flood.
Shield Worlds are essentially hollow planet-sized artificial structures, comparable to what we might call a "small Dyson Sphere". They might serve as shipyards. One of them, the "Sharpened Shield", is actually housed in a Pocket Dimension, the gateway to which is inside another Shield World built out of Sentinel robots (i.e small UCAV units). The Sharpened Shield itself has multiple Pocket Dimensions of its own, to store a big starfleet.
Halo: Cryptum describes other structures as well. Fortress-Class warships, and The Capital station, just to name a few.
The way they're described, it's highly probable that the Covenant capitol High Charity was a Fortress-class. The Forerunners had fleets of the things.
Precursors, on the other hand, are regarded by the Forerunner as Sufficiently Advanced Aliens. Their structures are all but indestructible for them, and only a Halo pulse can frag them. Why? Because the Precursors used sentience itself as a building material. Or, something. To be specific, Precursor structures are built using something called "neural physics", which completely baffles the Forerunners. The Precursors are apparently so advanced that they have long since abandoned a single form for their species: the Flood, the galaxy-spanning information network "The Domain", and the strange, virulent "dust" found by ancient humanity are all Precursors. Furthermore, some dialogue in Silentium suggests that the Precursors are older than the universe itself, and have in fact existed through multiple incarnations of the universe.
Some theories have the G-Man in the Half-Life series be one of these. He clearly fits the description as he is able to manipulate reality, stop time and teleport people into bizarre alien realms, all without twitching a muscle. He also appears completely unconcerned by the carnage going on around him.
At one point in the series, the Vortigaunts are shown to at least have some kind of power over the G-Man when they manage to successfully hold him off and keep him away from Gordon for some stretch of time. But what exact implications this has on the limits of the G-Man's power is never explained.
MOTHER 1 has Giygas, who is a sufficiently advanced alien — advanced enough to where the form of his attacks are incomprehensible, even to psychics. The sequel, EarthBound, upgrades Giygas to Cosmic Horror status.
The final boss of the first Shadow Hearts, Meta-God, is explicitly described as an alien so powerful humanity is on the level of ants compared to it. The purpose of The Very Definitely Final Dungeon is to call it to Earth so that it will lay waste to the planet.
Well, For Science!. Rather oddly, the Kreegan manages to be a major threat to the Ancients, to the point that they brought down the overarching Ancient civilization throughout a Galactic arm, while simultaneously being defeatable by a Lost Colony fallen deep into barbarism and witchcraft without said colony having to resort to scavenged Lost Technology or some new-found Achilles' Heel, if only on the planetary scale (the Kreegan are Planet Looters, and as far as can be told from the games, act independently from Kreegan forces on other worlds).
Averted and subverted with every other race. In Revelations, the turians just before the First Contact War described as being on roughly the same technological level as us. Most other races also dance on that line, and then there are some races like the krogan, vorcha, and drell that "hitchhiked" into space for one reason or another. Which is in turn justified because all advanced space technology is based on the technology of the previous spacefaring civilisations, all of which had a finite time to develop their technology before being harvested by the Reapers. Basicaly, having everything incorporate Mass Effect technology puts everything on an even playing field, at least until the masters of that technology come knocking.
The Xel'Naga from Starcraft. They're all about cosmic cycles, "star-forging", and re-creating themselves out of separate species that they engineer and eventually unite. All was nice and dandy until an Eldritch Abomination did them in by corrupting the Zerg, who Turned Against Their Masters, and the Xel'Naga haven't been seen since.
The Wave Existence from Xenogears, an energy being from another dimension that somehow created our own. It believes it is what the inhabitants of this dimension would regard as "God" but doesn't think of itself as such. Probably because it spent billions of years trapped in the Zohar Modifier.
The player in Spore can be this, from creating life on barren planets, painting crop circles to incite wonder and worship from primitives, uplifting civilizations to bringing nuclear from the sky upon hapless tribes.
In Assassin's Creed I the surviving members of the First Civilization were the basis for the deities of most religions, both due to their technology and the fact that they ruled over humanity before humankind rebelled. The Pieces of Eden have effects considered explicitly to be "magic" by those who witness them, though Altair concludes that it is simply sufficiently advanced — and supremely dangerous — technology. Among the noted abilities of the Pieces of Eden are mind control and immense amounts of technical knowledge (the Apples); telekinesis and mind control (the Staff); resurrection of the dead (the Ankh); healing severe wounds, disease, and genetic disorders (the Shroud); and telepathy (the Crystal Skulls). Some of the artifacts are capable of temporal distortion (the device responsible for the Philadelphia Event) or outright seeing into the future; one of the "senses" of the First Civilization was "knowledge" which apparently allowed them to know things that would be impossible to understand otherwise, and this apparently included the ability to see the future.
In the Marathon series of games, the S'pht'Kr probably qualify, the Jjaro definitely do, and Durandal achieves it by the end of Marathon 2.
Asura's Wrath has the Shinkoku Trastrium civilization, which are actually super-powered human cyborgs descended from Genetically altered humans, have a lot in common with this trope, with a Hinduism and Buddhism twist.
Galactic Civilizations has the Mythralar, who existed long before any other sentient life and one of whom created the Precursors: Arnor and Dread Lords. One of them is also indirectly responsible for the Altarians being Human Aliens. What happened to them is not known. Two different Victory Conditions result in your species becoming Sufficiently Advanced: either by absorbing enough Ascension Crystal energy or by doing so much research that you learn the secrets of the universe and ascend naturally.
The Prime Movers in Buck Godot are Sufficiently Advanced Aliens, and are stated to be omnipotent (at least they're very good at bending the laws of physics and geometry).
Lord Thezmothete is most likely one too. His abilities are never explicitly shown or mentioned, but he is mentioned to be a Class 1 Power (by comparison, an alien with the power to teleport entire planets around was classified as Class 8 and humanity — collectively, mind — is a Class 12 Power). He does possess some nifty technology at least, such as a waste disposal unit that creates miniature black holes and in his first appearance was able to make a battle fleet disappear without a trace.
Dragon Ball Multiverse: The Vargas, who organize the tournament. Also the guys from U19, who rely on technology to fight.
Subverted in The Salvation War. The demons and angel are very much insufficiently advanced to deal with modern weaponry. However played straight in that this is what they were when they first showed up in the Bronze Age.
Inverted for a period of time as well. Once humanity organizes a counterstrike against the demons and absolutely slaughters them, some of the demons begin to believe that humans have figured out how to use impossibly powerful magic and cannot be defeated.
Some of the most advanced technology in Orion's Arm is referred to as "clarktech" or "clarketech" in reference to this. Although it's not created by aliens, but by Sufficiently Advanced Terragens — the Archai and the higher Transapients.
Inverted in Land Games. The humans seem this way towards the indigenous natives. Some even worship Jayle as a goddess.
The Kankiscree, a species of reptilian aliens in the Global Guardians PBEM Universe, have had a space-faring, technological society for at least 70 million years. By the time the humans encounter them in 1985, their technology is firmly in the grasp of Clark's Law.
This video is rather interesting in its own right, but one of the claims it makes is the believe in "stair step evolution." That is, aliens came along and gave humanity little hints to get its evolution back on track. They also apparently built the pyramids and other religious architecture, and planted it along ley lines in an effort to raise the spiritual energy of humanity to high-level consciousness.
In Worm, one of these is the source of parahuman powers - in fact, said physics-breaking powers are vastly crippled versions of its own - and Scion is its avatar.
Kim Possible had the Lorwardians, a race of aliens who were not only giant, superstrong creatures, but they also possessed an arsenal of power world-destroying weapons. They were so advanced that it only took two of them to unleash an army of tripods and conquer the earth 'in the time it takes to order a pizza. They were only brought down by Drakken's new mutant plant powers destroying the army of walkers while Ron used his Mystical Monkey Powers to take down the invaders.
Sul, the Avatar Satis and Canaletto on Ōban Star-Racers. The Creators, on the other hand, may actually be gods.
"Bem" has probably the only instance in the entire franchise of a powerful alien looking after a planet of primitives, who appears to be genuinely wise and benevolent enough that Kirk doesn't automatically object to the situation on principle. Bonus points because the alien was voiced by Nichelle Nichols (Uhura).
Also the zookeeping Lactrans in "The Eye of the Beholder,'' who aren't exactly godlike, but are still an order of magnitude beyond Federation tech.
Ditto for the Vedala in "Jihad," described as the oldest known space-faring race.
Primus, and by extension his polar opposite Unicron, from Transformers. Primus created the Transformers, and his physical form is their homeworld, Cybertron. Unicron has altered a number of Transformers to his own liking, goes around eating planets, and transforms into a planet himself. Whether or not they're actually gods is entirely dependent on what segment of the mythos you're in.
Beast Wars has the Vok, the mysterious, skull-shaped aliens who police the space-time continuum and may have created the Earth as an elaborate experiment (and then tried to blow it up with a moon-sized Death Ray). According to some Word of God (their origins are never explained and the writers never really made up their minds on it) they might actually be hyperevolved humans.
Or they might be sentient robo-cancer post-Mind Hug.
And that's to say nothing of the Transformers themselves? Come on, they're Mechanical Life Forms capable of altering their very bodily structure that occasionally come back from the dead. In one episode of the G1 cartoon, they were actually mistaken for gods by an alien race.
Members of the First Thirteen, such as Vector Prime and the Fallen, have powers far beyond the abilities of other transformers. Vector Prime, for example, has the ability to manipulate time and space.
In Iron Man: Armored Adventures, Doctor Doom claims Dormammu (a demon in the original Marvel continuity) was an extra-dimensional alien. He goes so far as to claim his abilities and technology made him seem demonic, explaining why early humans believed him to be from Hell.
Mormonism teaches that God at one time existed in a mortal form similar to that of humans but was eventually "exalted" and now possesses a physical body similar to that of humans, but immortal and invulnerable to injury or disease. In the Book of Abraham, Kolob is described as a star that is "near unto [God]" and that has been set to govern all celestial bodies similar to Earth. (See Abraham 3:3) God is the literal father of our spirits and of those on all the other worlds that he created, which are described as being "without number" (Moses 1:33,35). After the second coming of Jesus Christ, everyone who has ever lived or died will be resurrected with perfect, immortal physical bodies similar to God's, but only those who have fulfilled all of the requirements of the Gospel and faithfully endured to the end will obtain "exaltation", entering into the highest degree of Celestial Glory (i.e., the kingdom of God, or "the glory of the sun") and in effect become "gods" themselves, possessing all of God's wisdom and power and becoming able to create their own worlds. (D&C 76:50-70, 92-96) This doctrine, known as "eternal progression", was summarized by former President of the Church of Jesus Christ of Latter-Day Saints and Mormon prophet Lorenzo Snow as: "As man is, God once was; and as God is, man may become."
The satirical Church Of The Sub Genius refers to Jehovah-1 as "An evil Space God from some corporate Sin Galaxy", and has an entire hierarchy of more-or-less omnipotent species of aliens, but also claims to believe in the "Elder Gods", and "possibly the One True God, but He ain't talking".
Physicist Frank J. Tipler advocates Omega Point theory, in which it is necessary that Sufficiently Advanced Aliens (or Sufficiently Advanced Humans) are not merely indistinguishable from gods, but become/create (it's complicated) God.
The idea of "Omega Point" as the point of ultimate human perfection was originally conceived of by French Catholic priest and evolutionary biologist Pierre Teilhard de Chardin!
Arthur C. Clarke stated that if we ever find intelligent alien life they would be "apes or angels, but not men." The reasoning being that humans spent the vast majority of their history in the stone age, but since the discovery of agriculture just 10,000 years ago technological advancement has accelerated at an almost exponential rate. So the statistical likelihood of contacting a technological species before they hit The Singularity is virtually nil.