In Legend of Galactic Heroes, religious beliefs are close to non-existent, which is explained as a result of people becoming disillusioned over religion after a nuclear holocaust mentioned in the backstory. The only organised religion present in the series, the Terraist Church, turns out to be a Path of Inspiration which aims to revive Earth's past glory through subversive actions such as assassinating key figures of the galaxy.
Religion is rarely mentioned in the classic Universal Century timeline of Gundam. In fact, the UC calendar was originally established in order to invoke this trope and usher in an utopian agefor mankind. There is still room from any number of fringe cults but these mostly have political ulterior motives, such as the Zanscare Empire in Mobile Suit Victory Gundam or the myriad manifestations of Zeon ideology.
In the English Dub at least, in Code GeassLloyd lightly teases Suzaku about how the Japanese still believes in such superstitions.
In Warren Ellis' Supergod, faith is stated to be a biological flaw in human neurology that enables group behavior without the enlightened self-interest that should preclude it; a "narcotic response" to the concept of a higher power. This means most of us will follow leaders based on their ability to evoke that response rather than their ability to encourage survival. It also means that most of us would be quite willing to surrender our free will to powerful forces that don't even see us as bacteria. You can guess how that turns out.
Eugenesis: The people of Cybertron have taken on this attitude after the first time Unicron showed up to eat everyone, with "theo-scientists" pouring out of the woodwork to calmly disseminate every aspect of Cybertron's religious texts. Of course, even they haven't figured out how the Matrix functions. And they become oddly quiet when the subject of the built-in killswitch every Cybertronian has comes up.
In Star Wars: A New Hope, where an Imperial Officer implies that the Force is regarded as "ancient mythology" in a pejorative sense:
Darth Vader: Don't be too proud of this technological terror you've constructed. The ability to destroy a planet is insignificant next to the power of the Force.
Admiral Motti: Don't try to frighten us with your sorcerous ways, Lord Vader. Your sad devotion to that ancient religion has not helped you conjure up the stolen data tapes, or given you clairvoyance enough to find the rebels' hidden fortress ...
Darth Vader: I find your lack of faith disturbing.
Stanislaw Lem's Solaris lapsed into painfulness: the protagonist's brooding about how humanity has not improved in any way is in the immediate company of the protagonist's brooding about how humanity has outgrown any foolish notions of God. However, in Lem's Fiasco, the crew of the expedition that tries to contact with an alien race includes a priest, who's portrayed positively. This is standard with Lem, really. He was writing in communist Poland, and one of his very first books was Soviet propaganda. Solaris was intended more to be about how humanity would react to meeting a very, very alien alien. Or possibly how they would take finding out that God is surprised to know we exist if you must make it symbolic. Just remember that Lem knowingly set out to use certain of the alien tropes as anvil targets...
In 3001: The Final Odyssey, the Earth of the titular year has long since abandoned religion. It's said that everyone is either a theist or a deist, as defined: the theists say there's at least one god and the deists say there's at most one god.
The Light of Other Days, co-written with Stephen Baxter, had a device that could see into the past; among others, Moses didn't exist, having been a merger of several different historical personages. Jesus did, but was just a good person who inspired people, rather than a miracle-maker.
Childhood's End, similar to the above example, the visitors give humans a device to see into the past. Apparently, every religion save Buddhism becomes discredited. Also, the visitors look like stereotypical devils; it turns out they are heralds of a change so monumental it echoes back through human history, causing the "devil" image in the first place.
The Fountains of Paradise, about the building of a Space Elevator, in which humanity's First Contact with an alien AI had the AI disprove the works of Thomas Aquinas, and possibly Christianity itself(!). And that was all in the exposition. There is one religion left practicing (a Buddhist-type), but it leaves its monastery when the yellow butterflies reach the top of the hill it's on, simply because they were prophesied to do it. It is mentioned that Vatican still exists as a center of Catholicism, but suffers from severe financial troubles, implying that the number of practicing Catholics is minuscule.
The closing stories in the Rama books, on which Clarke either collaborated or wrote himself, subvert this. The setting has humanity already in religious decline by default, however the very end of the series presents not only possible evidence for the existence of a divine being such as God, but an explanation for his laissez-faire attitude to dealing with his creation.
In the advanced cultures of Isaac Asimov's Foundation trilogy most of the main characters are supposedly atheists, and the leaders of Terminus certainly are, but outside Terminus religion itself survives, even if it's used as a tool of control at times. Over time though, Hari Seldon assumed an almost religious significance to the people of Foundation, to the point where many of them had a decidedly irrational belief in the infallibility of his predictions.
The Second Foundation trilogy (written by modern authors) portray the different aspects of Robot philosophy (Asimov linked his Robots and Foundation series in later books) as being akin to religions, including "Calvinists" (which for religious scholars is wonderful as these are the conservative/catholic analogues), and several other sects who have their own interpretations of the body of doctrine that is the Laws of Robotics.
His "Nightfall" is even more interesting. The scientists had worked out the cause of the periodic devastation and the things called "stars," and the religious fanatics were deeply offended — and also had a much better idea than the scientists how serious the matter was.
Asimov also played with religion in some of his robot stories, including one where a robot that was activated on a space station believed the station's machinery was a god, called it "the Master," and believed Earth was a religious fiction designed for the small-minded humans.
In the Culture novels, the Culture looks at religion as a delusion which you should be sympathetic about. This viewpoint runs into trouble in Look to Windward, where the "enlightened" races are irritated and nonplussed that whether or not the Chelgrian heaven existed before, it demonstrably exists NOW.
Even this concept is played with in Surface Detail. Due to mind state copying technology and sophisticated virtual reality environments, it is now possible to make any number of afterlives as indistinguishable virtual reality simulations. Hell (or it's closest equivalent for each religion) is the most commonly created. It proves to be a contentious issue in galactic politics, with the Culture not taking an active role. Initially...
While it's never said outright, on several occasions the books separately point out the two facts that 1) Culture Minds (and their attitudes, i.e. this trope) are to a large extent shaped by the culture of their designers, and 2) it's very, very difficult to actually describe one without using the G-word.
The Algebraist features a future religion that actually fits in a science fiction setting. The dogma is that the universe is a simulation and the goal is to end the simulation by getting enough of the participants in the simulation to realize they are in one. The main character of The Algebraist seems skeptical of this religion, though. The simulation hypothesis is also brought up in the Culture novel Matter, without a religion surrounding it. See Simulation hypothesis for the real-life example.
Alfred Bester's The Stars My Destination didn't explicitly say that all religion was outmoded in its society, but Christianity was illegal, and pictures of nuns praying was considered equivalent to pornography.
A Case Of Conscience toys with this, which features a totally agnostic if not atheistic alien race that also live in a perfect world and society, faced against a bombed-out, nuclear-fried, and heavily Catholic Christian human race. The priest included in the first contact mission considered that society a danger to humanity precisely because it was a rationalistic atheistic utopia; unfortunately, he'd already befriended one of those people before he made the decision. The alien world is blown up by the latter either using the wrong space telescope or due to an exorcism.
Resoundingly averted in John Maddox Roberts' Cestus Dei/The Strayed Sheep of Charun. In this future, known space is dominated by the United Faiths, made of the Big Five religions and apparently some lesser ones. The main plot involves Franciscans and Jesuits working to reclaim a "system" (actually a multistellar state) which has reverted to paganism. (And even worse, making androids, which all the UF regard as "soulless" horrors.)
Giants Star by James P. Hogan has a particularly fierce instance: the protagonists deduce the existence of an alien Ancient Conspiracy to suppress human progress as a reasonably parsimonious explanation for the continued existence of religion in modern times.
Anne McCaffrey's Pern is a world without religion. The expressions "Jays" and "by all that's holy" are still in use, but only as swears.
Her Talents series plays this mostly straight. Those few protagonists who espouse a belief in a higher power are, at most, vaguely Deist. Those who are openly devout are almost always portrayed as mentally unstable troublemakers. Organized religious populations are shunted to backwater worlds where "the harm they can do is minimized" (or words to that effect).
With the elves, it's more along the lines that they believe in logic, and pertaining to their logic, there is no such thing as a god. Oromis is somewhat reasonable about the whole matter. Arya, on the other hand...
Played straight by the Edenists and averted by the Kulu Kingdom in Peter F. Hamilton's (sci-fi) Night's Dawn Trilogy. They are the two biggest players and the two biggest rivals in the Confederation — the former are all atheists and the latter staunchly Christian. However, the Edenists' philosophy and way of life lead to the closest thing to paradise as you can get, and they're also the only human civilization able to fully resist the possessed...
Also, in Hamilton's Commonwealth Saga, religion is for the most part "weddings and funerals" only. However, in the distant sequels of the void trilogy, a massive religious pilgrimage is the source of the main conflict of the stories.
Neal Stephenson's Anathem features a world in which a group of secular monks wall themselves away from society and study pure logic, science, philosophy and art. Although they are not officially atheistic, few members hold onto any religious beliefs. In the outside world, religions rise and fall unnoticed. While venturing in the outside world, monks can quickly reduce any religion they encounter into one of a number of basic categories so that they can avoid causing offense. Religious non-monks are mostly presented as morons, while the brightest are good enough that they aren't completely humiliated when they try to debate with a monk.
Sort of both used and averted in the Humanx Commonwealth novels, where humans and thranx and several other species look to the United Church for guidance. It's a synthesis of the basic ethical tenets which all humanx religions share, shorn of world- or culture-specific trappings that would fall under this trope's "superstition" label. Essentially, Unitarianism's gone multispecies: they don't attempt to define or disavow a Higher Power; they just agree that if there is such a thing, this is how he/she/it/they would surely want folks to live, and if there isn't, it's still good to live that way.
In the Uglies series, the people of the future sarcastically refer to gods as "invisible superheroes in the sky". There are some groups that try to bring religion back, but it isn't catching on. In all, the books don't pay very much attention to this, and it's mostly a detail to help show how different society has become since our time.
Roger Zelazny enjoyed making far-far-far-future societies where humans had become Sufficiently Advanced Aliens and taken on the roles and power of ancient gods. In Creatures of Light and Darkness, they had taken on the personae of Ancient Egyptian gods (including managing afterlives). But one of the most prominent characters was Madrak the Mighty, a warrior-priest "of the non-theistic, non-sectarian sort", whose personal religion was based on an agnostic's deity (another character referred to him as a "holy ambulance-chaser"). When Set the Destroyer pointed out to him that Madrak had just aided in the destruction of the Nameless, an Eldritch Abomination from beyond the universe, which perfectly fit the definition of Madrak's agnostic God, the idea that his god existed - and he profited by Its death - made him suffer a crisis of faith.
John C. Wright's The Golden Oecumene never says anything one way or the other about religion, but it's somewhat odd that in a setting where characters are defined heavily by their philosophical beliefs, the only person who engages in any form of worship or mysticism is a bit character whose philosophy is never explained.
In Divergent it is implied that the Abnegation faction (a faction of society that lives much like the Amish) is the only section of society that still believes in God. However, its sequel Insurgent shows that the Amity Faction practices some sort of naturalistic religion.
Downplayed in the Star Carrier series. Due to Islamic terrorism having been largely responsible for World War III in the backstory, all faiths have to abide by a pledge called the White Covenant that makes many religious practices (chiefly proselytizing and conversion by threat or force) violations of basic human rights. It's mentioned in book four that being religious and having it listed in your military jacket can seriously hamper your career.
Averted in Mikhail Akhmanov and Christopher Nicholas Gilmore's Captain French, or the Quest for Paradise, which takes place about 20,000 years in the future. Humanity has settled thousands of worlds. Yes, some of the worlds view religion in this manner, especially on the planet Tranai ruled by "humane communism". Some other worlds are ruled by theocracies, such as the Holy Archonate on Murphy, which is recovering from a comet strike. According to the titular captain, theocracies are an inevitable part of the "democratic cycle". Any planet that strives to have a democratic government will eventually become corrupted and become ruled by a dictator. After a period of tyrannical rule, a civil war will tear the society apart, giving rise to a theocracy. After the people get tired of praying and casting their eyes downward, the theocracy will be overthrown by yet another democratic government... and so on. According to French, en enlightened monarchy is the only stable form of government in the long term (the "long term", in his mind, is measured in millennia).
Jean Delumeau narrates in his Sin and Fear: The Emergence of the Western Guilt Culture, 13th-18th Centuries that his trope was one of the objectives of the Inquisition. There were several regulations against practices that were considered superstitious, like usage of amulets and anything magic-related, so much that, in trope terms, they were enforcing that Religion IsNOT Magic.
In an episode of Star Trek: The Original Series, Kirk tells Apollo (or at least a being who claims to be Apollo) the following: "Mankind has no need for gods. We find the one quite adequate." Exactly whether he's claiming everyone follows a generic monotheistic religion or that everyone has just given up polytheism is unclear; probably the former, knowing the probable standards of NBC and society at the time (Robert Justman confirmed the line was required by NBC's Broadcast Standards). Kirk also reveals a more spiritual side at the end of the episode when he tells Bones "They gave us so much...would it have hurt us to burn just a few laurel leaves?"
The Klingons are stated to have once had gods, but their distant ancestors killed them all off because the gods proved to be more trouble than they were worth. In spite of this, they have an underworld ruled by "Fekh'lar." One episode of The Next Generation deals with Kahless, a divine, Christ-like ancestor figure in Klingon history. There is a shrine of Klingon priests who await the return of Kahless and Worf has had spiritual visions of Kahless speaking to him in the past. Generally, their faith in Kahless is treated in a positive light.
In "Day of the Dove", Kirk tells Kang, "Go to the Devil!" Kang replies, "We [Klingons] have no Devil... but we are very familiar with the habits of yours." Cue use of torture.
The most Anviliciously atheistic Star Trek ever got was the third season TNG episode, "Who Watches the Watchers"; a group of Federation scientists are using holographic technology to watch a primitive Vulcanoid culture that has apparently abandoned religion. The Federation equipment breaks down, revealing their existence and "magical powers" to the locals, one of whom declares they must be gods and tries to restart the Old Time Religions. Picard takes another local up and explains that the Federation are merely Sufficiently Advanced Aliens, not gods. The episode then goes into Author Filibuster mode; the time humans had religions of any sort is referred to as "the dark ages of superstition and ignorance and fear." Afterward, an away team goes down to the planet to explain how irrational it is to believe in gods because they never show up or tell believers what they want, and that believers are left putting their faith in what other mortals tell them.
In "Where Silence Has Lease" Picard is asked by Data about death; interestingly his philosophical answer seems to hint that while he isn't personally religious he seems to have equal problems with a purely atheistic view.
In "Déjà Q," when Q, who has been turned into a human, sarcastically contemplates becoming a missionary, Data states that such a line of work would be admirable, implying that there are still humans who view religion positively.
Deep Space Nine is a 7 year mix of affirmations and aversion/subversions of this Trope. The Commander of the station was declared to be alien Jesus in the first episode, later finding the alien Gods to confirm it, then having visions and becoming a god himself.
In "Dagger of the Mind", and in Star Trek: Generations, it is shown that they still celebrate Christmas and actually call it that, instead of the current contemporary habit of "Holiday Season". Obviously, in the 23rd century, regardless of the actual Christian content observed, they have removed all of the current commercialism from the holiday. In "Data's Day", Data mentions that the Hindu Festival of Lights was still observed.
It's very much worth noting that many Christian viewers never had any problem with the Original Series, because after all, Kirk was running around the universe toppling transparently false gods (including Apollo himself!—while citing the virtues of monotheism both in that episode and in "Bread and Circuses") and that the computers like Landru and Vaal are literally the ultimate form of idolatry, the worship of physical manmade gods. Despite Roddenberry's penchant for Kirk vs. god-thing-of-the-week plots, open hostility to monotheism didn't come to the fore until Next Generation. The closest the original series came to this was probably "Return of the Archons," and even that one ended with Kirk taking down yet another computerized idol.
Kirk's Enterprise has an interfaith chapel. It appears in the wedding ceremony (which Kirk, just like a naval captain, gets to officiate) in "Balance of Terror," and is mentioned on the list of sets in the Original Series's 1960's writer's guide. The wedding ceremony includes the phrase, "in accordance with our laws and many beliefs."
One of the many Planet of Hats that Kirk et al visited was a rather Roman Empire-based one, where a former Starfleet captain acts as the First Citizen. They also met a small group of people that were a mix of La Résistance and worshipers of "the Sun". After the fact, Uhura ponders if they were talking not of the Sun in the Sky, but the Son of God.
Some could see Stargate SG-1 as one big Take That against organized religion. The eponymous team spends at least half of the plot convincing primitive groups that their gods are fake and should forget about them, even the ones with the characteristics of actual gods: they are, after all, merely sufficiently advanced aliens posing as gods, either snaky parasites out to exploit humans or well-meaning Little Gray Guys trying to help. With the Ori, things are more blurry: they actually qualify as gods according to one Real Life religion and would do so in most fantasy series, but writer intent evidently considers them false gods as well. After a few episodes of dealing with ridiculously headstrong groups, the team basically settles on "Just because they're powerful enough to claim godhood, doesn't mean you should actually worship them!"
Many other episodes reference religion directly in subtle or not so subtle ways, like "The Sentinel", where the Latonans refuse to evacuate in the face of an alien invasion, constantly referencing their "highest law".
Things were handled a little differently in "Red Sky". A planet is doomed and the people refuse to leave as they think their death is the will of the gods (specifically the Asgard, although they don't know who they are specifically). While Jack is more than willing to destabilize their belief system, Daniel tells him that while the possible existence of their gods is not important, the belief is. At the end of the episode, the resolution is deliberately left unclear. It may be that the Asgard fixed the problem, but Daniel wonders if it's possible that a higher power did intervene.
"Icon" featured an incident similar to the aforementioned TNG: "Who Watches the Watchers". The arrival of SG-1 on the planet Tegalus causes a Goa'uld-worshiping extremist faction to gain in popularity, eventually starting a civil war that aggravates a cold war. Difference is, the SGC views it as a purely military/political problem that's keeping them from rescuing Daniel, who was trapped on Tegalus by the war.
Slightly different from the norm, the episode "Demons" features a planet of Christian-ish people where the Goa'uld in question is pretending to be Satan rather than God, with Unas as his demons, but despite Teal'C mentioning that he does not believe any Goa'uld is capable of the "kindness expressed in your Bible" the plot goes largely as standard. The villagers are firmly in The Dung Ages and still practice trepanning, the priest is a pompous jackass who exploits their fear to keep his power, and they refuse to accept SG-1's help, imprisoning them and putting Teal'C through deadly "witch trials" (though they went for the more historically accurate Drown The Witch instead of Burn the Witch!). In the end the Unas is killed (by the one villager who believed SG-1) and they no longer believe it's a demon.
Stargate Atlantis has plenty of Take That moments against religion, like "Poisoning the Well", where the scientific search for a Wraith immunity drug has become a religion, with libraries of knowledge as a church analogue and a famous scientist's lab notes are a sort of holy text. The real clincher is the population's eagerness to take the unsafe product, even when they know exactly how unsafe it is.
Another episode has one of those weird unclassifiables in the form of "Sanctuary". There, they find an incredibly primitive world untouched by the Wraith, whose inhabitants lead idyllic lives, all of which they attribute to their Goddess, Athar. Said God, it turns out, is actually an ascended being that takes mortal form to serve as Athar's high priestess. So while they are being deceived, they also really ARE protected and cared for by a nigh-omnipotent being.
The Twilight Zone TOS episode "The Obsolete Man" was set in a future society where religion had been outlawed. Only one man still believed in God, and was sentenced to death for being obsolete. He was given the choice of ways to die. He chose to die by bomb on live television. The high official who sentenced him to death came to speak with him, and was informed that the door was locked. He began to panic, and shouted, "In the name of God, let me out!" The condemned man did let him out — in the name of God. The final scene was of the official being sentenced to death... for being obsolete.
During Russell T Davies' run, there was little to no mention of magic or religion, and when it was it was usually proven to be science based or very vaguely described. In an interview, Davies claimed that he had banned God from the writer's room, wanting to depict a future where religion had just died out. "[R]eligion is banned on Platform One. Yes, I'm deeply atheist. If they haven't reached that point by the Year Five Billion, then I give up! When did the Doctor do that speech about believing in things that are invisible? It's Episode 5, isn't it? That's another bit of atheism chucked in. That's what I believe, so that's what you're going to get. Tough, really. To get rid of those so-called agendas, you've got to get rid of me."
And with Davies' departure, religion has returned to the series in a major way. The main villains of Series 5 and 6, the Silence, are revealed to be some type of intergalactic religious order and the Doctor himself gets along quite well with the chief Priestess of the Galactic Papal Mainframe.
The original series is filled with religions and cults, or just individual characters with faith, in all places and time periods who turn out to be deluded, deceived, plain wrong, or outright villains. A very common plot is to have the Doctor get caught up amongst people worshipping a piece of technology/Sufficiently Advanced Alien/Eldritch Abomination as a deity, and in order to survive he has to convince them not to worship it and/or outright kill their "god". The whole point of the character Leela was to contrast her savagery and superstition against the Doctor's pacifism and scientific knowledge, with their first scene in "The Robots of Death" having the Doctor explicitly tell Leela that magic doesn't exist.
The Doctor, one of the oldest, most intelligent and best-traveled beings in the universe more or less says in "The Satan Pit" that he doesn't believe in God or any sort of higher power (or at least he's never run across anything to convince him of the existence of such a power). Granted, his people the Time Lords were so powerful most civilisations in the universe would consider them gods, so he has a very different perspective on the issue compared to most.
Farscape takes an interesting perspective on religion for a sci-fi show: though it doesn't discuss religion extraordinarily often, it does have practitioners of various alien religions among the crew, some of them quite devout. Plus, the show also demonstrates that gods and magic really do exist in their universe, some of them more visible than others - like the Builders that Moya worships. The Peacekeepers, on the other hand, play this trope straight, with an entire episode, "Prayer", devoted to Aeryn recounting the ancient legend of a Sebacean goddess (implying that they no longer believe in gods in the present day) and praying to her for rescue; for added desperation points, Aeryn notes that the reason this particular goddess doesn't have any followers anymore is because she killed them all on a whim.
A sketch on The Kids in the Hall featured a futuristic society that celebrated Bellini Day in which the characters referred to a time period where mankind was so stupid they actually believed in someone named God.
Babylon 5: In "The Lost Tales" mention is made of how religion has been declining since humanity went to space and made contact with other races, but it's still has a considerable presence in Earth-influenced space and among the alien races. The straightest example of this is probably Lorien, who says his people lived so long they simply had no more use for such things. The rest of the characters tend to play with this.
Cthulhu Tech contains a rather bad example. Christianity and Islam are gone; it's not really expounded upon, they're just gone. Presumably, the very real and somewhat provable existence of the old ones made everyone less interested in religions that have a very specific world view that excludes them.
The Tau seem to exhibit divine worship of their Ethereals, but that is more obeisance to their leaders than religion and otherwise have no belief in anything "magical" or "supernatural", including the very real daemons and other things that inhabit the warp. Interestingly, they are by far the most socially and technologically progressive faction in the setting (which, granted, isn't saying much).
The Eldar believe in the existence of their gods and invoke the power of one on a semi-regular basis, but they don't worship them and most of the time they use their names similar to how many English-speakers today use "oh my god". This is because their gods were eaten by a Chaos god and there is no real point to much of their religion anymore. There are exceptions though:
Cegorach the Laughing God escaped being consumed, but only the Harlequins worship it.
In Eclipse Phase many religions didn't survive the Fall and the exodus via Brain Uploading from earth, but new faiths arose to fill in the gaps. The most common being Neo-Buddhism, Buddhism combined with Transhumanism where uploading is seen as a form of reincarnation and the emphasis is on lessening suffering rather than escaping it. Though oddly Islam was able to adapt to uploading when the other Abrahamic faiths largely couldn't. And the Catholic church is still influential in the Jovian Junta, with its large population that managed to escape earth in their original bodies.
Baten Kaitos Origins twists this trope. It starts off with a fairly simple "science = evil" message, but then it turns out that in the distant past people became practically addicted to the supernatural, and so a bunch of siblings in the past decided to try and stop them from being turned into pure magical essence by making a Deal with the Devil to gain even more supernatural powers in order to overcome what they were fighting, but then they all get sealed into the End Magnus from the first game, but then it turns out that the process that gave Sagi the supernatural power of one of the siblings was a scientific one, but he then uses that power to save the world. While getting a boost from the spirits of the dead siblings, no less. In short, rejecting the supernatural and focusing on science - or vice versa - is a Very Bad Thing, and the best way to live is with both in tandem with each other.
Deus Ex: Invisible War is a Double Subversion; according to its backstory, the aftermath of Deus Ex led to The Collapse, in which most people had their faith shaken to the point this trope almost got played straight—until The Order popped up, uniting all of the old faiths into one syncretic philosophy. Later, however, it's revealed that The Order is just one of two fronts for the Illuminati, and is part of their method of controlling polar opposites of society.
In Metroid Prime 3: Corruption, Samus visits the planet Bryyo, which is covered in the ruins of a golden age. The Reptilicus people there originally had magical powers. Then, some of them learned how to use technology, and they decided that this was cooler than "primitive" magic. The Lords of Science honked off the magic-using mystics, and there was a big magic-vs-technology war that tore the planet apart. Literally. There are bits of the planet that had to be chained to the surface (though those might be wrecked spacecraft made of stone). It could be said that the Lords of Science technically won, because a few of them were able to recognize the planetary damage and stabilize the planet, though it lead to them revealing their secret location, and thus being wiped out by the mystics. Without the Lords of Science, the remaining Reptilicus devolved into (magical) barbarism.
Averted with the Chozo, who made balance between the technological and mystical aspects of their society a priority, so much so that it's almost impossible to tell where the science ends and mysticism begins in their technology. (Indeed, the Chozo actually warned the Science lords that they needed balance between the two. They didn't agree until far too late.)
The University of Planet faction is the ideological antithesis of the Lord's Believers game mechanic wise, but the faction leader Prokhor Zakharov is especially into this trope, as a number of quotes from him for technological advances reveal. According to the prequel short stories, he and Miriam Godwinson (the Lord's Believers faction leader) do not get along well, even back on the UNS Unity.
The Human Hive faction explicitly seeks to invoke this trope. It's faction leader Shen-ji Yang's social experiment, amongst other things, as he seeks to eradicate belief in higher powers and replace it with an atheistic police state (this is his explicit agenda in-game).
Aside from the Lord's Believers, Gaia's Stepdaughters are noted to be a religious society focused on coexisting with nature, the Cult of Planet is obvious, both of the Progenitor factions smack of taking their dogma to the point of religion.
Star Ocean 1 has Ronixis, who claims that humanity has moved beyond religion. However, finding himself in the backwards world of Roak, and confronted with the existence of magic, which he'd hitherto never believed existed, he finds himself re-examining his views. The sequels make clear that magic is nothing more than advanced science, however. The third game even simultaneously proves that God exists and provides a scientific explanation for the big jerk.
Both played straight and averted in the StarCraft universe. Background material mentions that upon taking control of Earth, the United Powers League(later becomes United Earth Directorate) promoted state Atheism, banning or co-opting all religions and exiling or killing those who didn't adhere (alongside political prisoners, cyber-deviants and other undesirables) in an effort to stamp out the things that have divided the human society. As a result, the territories of the UPL/UED are non-religious while the Koprulu Sector is teeming with religious groups ranging from mainstream Christianity to Crystal Dragon Jesus and to even stranger Cults and movements.
The most advanced race in the setting, the Protoss, nearly killed themselves before the religion/social structure of the Khala was established, and while it's lessened in importance with the acceptance of the Dark Templar, it's still hugely important to most of the race.
In BioShock, Andrew Ryan considers religion an obsolete and harmful superstition "people of tomorrow" should have no need for. He strives to eradicate religion in his Objectivist utopia and declares that smuggling religious texts to Rapture is a crime punishable by death. The experiment however goes terribly awry.
Both used and averted in the X-Universeaccording to the X-Encyclopedia. About half the Argon consider themselves "spiritual" but don't believe in any particular deity, while most of the rest are atheists. But since they believe in tolerance, the Argon place no stigma on being religious. The Boron have no organized religion and no omnipotent or creator deities, but some believe that after death they will live on in the presence cloud of theAncients. Averted with the theocraticParanids, whose religion permeates every aspect of their lives. The Split are the straightest example, viewing their old religions as primitive superstition. No word on the Teladi or Terrans.
In backstory of Homeworld, the Kharakians near-entirely abandoned religion after generations of religious wars devastated their already small population, part of a unification of the planet's disparate tribes that placed reason and scientific understanding above all else. Religions still existed to some extent, however their few serious adherents were considered delusional at best and dangerous fanatics at worst. That is, until Kharak wasbombed into oblivion; afterwards the survivors experienced a slight resurgence of religious belief, such as the members of Kiith Somtaaw in Cataclysm.
In Mass Effect, humans as a whole still follow lots of religions, but space-faring humans don't, with Ashley implying that she's seen as eccentric for even mentioning her religious belief. Meanwhile, the hanar worship the very real (though long-extinct) protheans, and the most popular asari religion is revealed to be entirely based upon contact with Protheans by their primitive ancestors, heavily implying that many ancient religions may be the direct result of alien contact, misconstrued or misremembered by the populations they affected. The turians, salarians, and quarians, though, avert this entirely. The turians believe in a form of pantheistic animism (though some turians are exploring other religions which mesh with their world-view, like Zen Buddhism and Confucianism), quarians are generally atheist but hold their ancestors in a reverence which sometimes borders on worship and salarian religion is never explored. When asked what their religious viewpoint is, Shepard can either confirm or deny any religious leanings, or simply note;
Shepard: Everyone has the right to believe what they want. Says so on the Alliance charter... only in fancier words.
Mordin Solus is a particularly strong aversion of this trope. He's a salarian scientist, but his guilt over helping to modify the krogan genophage led him to explore religion, with the implication that he still follows an (unnamed) salarian religion. The Lair of the Shadow Broker files on him mention that he was a guest on "The Facts Of Faith".
Inverted in the FreeSpace game mod Blue Planet. A major part of the story is that mysticism and spirituality are creeping back into society, and there exists at least one Sufficiently Advanced Alien race that is heavily spiritual (or at least, expresses themselves in a spiritual manner). The title of the campaign's first release, "Age of Aquarius", references this: it refers to an age in which, realizing that neither religion alone or science alone has all the answers, people turn to a fusion of the two to reach true understanding.
Used but mostly averted in Startopia. An entire race, the Zedem monks, have converted to the same religion and only two of the games nine races don't pop into a temple occasionally. The only exceptions are the hedonistic sirens and the scientific Turakken.
In Fire Emblem Awakening, this is what Walhart wants the world to be like: advocating the idea of a militaristic and atheistic new world order under his rule to bring an end to war and strife. During their Support conversations, the Player Character admits that, while Walhart might be onto something, his world would be no better than a tyranny populated by forcibly-indoctrinated servants who've all been bulled into submission. In response, Walhart agrees - reasoning that, because he lost to the Avatar, he must clearly be in the right.The Hero Chrom also acknowledges Walhart's vision but rejects it on similar grounds - resolving to unite all peoples of all faiths (or lack thereof) by touching their hearts rather than forcing them to bend the knee.
This is how Actraiser ends. By defeating the local God of Evil, the Master has ensured that humanity can stand on its own without his help. The last scene depicts a statue of the Master crumbling to dust.
Inverted by Caligula of The Law of Purple; instead of an advanced culture that once had religion but derides it as worthless now, there was almost never any organized religion to speak of and parts of the population are only now discovering it. However, most Caligulians view religious groups as nothing more than cults and consider them highly abnormal.
Averted in the Schlock Mercenary universe. Religion is alive and well among many different cultures, and the Tagon's Toughs have their own chaplain (Reverend Theo). In his first appearance, comic author Howard Tayler included an editor's note stating that this trope is what's "foolishly optimistic," not religion.
Berandas: Don't you understand? We are the gods' unwanted children. We are the castoffs, the forgotten. And instead of following some doomsday cult, believing ourselves lost and hopeless like the Grey Cult, or clinging to some decayed bloodline like the Crimson Coalition, we will stand and fight for humanity! The gods don't like our choice of allies, our rising technology? They can burn for all I care, they have never helped us.
Parodiedrather savagely in the South Park episodes "Go, God, Go" and "Go, God, Go Part XII." Cartman awakens in a Hollywood Atheist future where Atheism has replaced religion. Religious factionalism and conflict have been replaced by equally trivial Atheistic factionalism and conflict. People shout things like, "Hail science," "science dammit", and "Science H. Logic!" instead of their religious equivalents. Ultimately the episode is about how atheists are just as susceptible to stupidity as the followers of any religion.
In an episode of Family Guy a lack of religion allows the U.S. to progress technologically by a thousand years, though the arts had stagnated for a similar amount of time.
Similarly, one episode of American Dad! is set in 2045, with the present referred to as "when people still believed in The Bible."
In Justice League, Hawkgirl comes from an advanced alien civilization which gave up religion eons ago (because their god was an Eldritch Abomination who demanded their souls in sacrifice), but after a certain episode she comes to believe that there is… something good… out there.
State atheism is an attempt to invoke this trope, which seems to lead to a considerable amount of Utopia Justifies the Means. Since Karl Marx viewed religion as a tool of the bourgeoisie, communist countries have done this as a matter of course. It tends to end up as replacing the worship of a god with the worship of the country's dictator or the worship of communist founders (including Marx himself). However, state atheism is actually older than communism, having first been attempted in revolutionary France as the Cult of Reason, busts of revolutionary Jean-Paul Marat briefly replacing the Catholic icons in the churches. Deist Maximilien Robespierre replaced this with state deism in the Cult of the Supreme Being, and having statues of the Goddess Liberty set up. This was hardly better, and the government actively persecuted Catholics, especially clergy, who opposed it.
The Soviet Union tried multiple times to invoke this trope through anti-religious campaigns, and by 1982 only 20% of Russians actively practiced religion, with a third declaring themselves atheist or non-religious. A few decades after the fall of the Soviet Union, a 2012 survey found that only 13% of Russians identify as atheists or non-religious.
Ironically, as people started to give up on the idea that religion would fade away over time, religion began to fade away in the younger generations in the developed world - an estimated 16% of the global population is nonreligious.
In the United States irreligion has grown to be the second largest "religious" affiliation after Christianity, with a third of young people self-identifying as such, compared to only 15% of baby boomers and single digit percentages of those from prior generations.