The "colorization movement" in Flatland by Edwin Abbott Abbott, where, after color is discovered, the lowly triangles and squares make themselves more interesting by coloring their edges. Color gets banned by the government because polygons start using color to sneak into the upper class by pretending to have extra sides.

The Agnostic's Prayer (Roger Zelazny, Creatures of Light and Darkness, © 1969)

Insofar as I may be heard by anything, which may or may not care what I say, I ask, if it matters, that you be forgiven for anything you may have done or failed to do which requires forgiveness. Conversely, if not forgiveness but something else may be required to insure any possible benefit for which you may be eligible after the destruction of your body, I ask that this, whatever it may be, be granted or withheld, as the case may be, in such a manner as to insure your receiving said benefit. I ask this in my capacity as your elected intermediary between yourself and that which may not be yourself, but which may have an interest in the matter of your receiving as much as it is possible for you to receive of this thing, and which may in some way be influenced by this ceremony. Amen.

Walter Miller's A Canticle for Liebowitz and how the religion blends traditional religion with a post-apocalyptic wasteland. Definitely recommend if you're a 40K fan.

Bokononism from Cat’s Cradle by Vonnegut

The folk who travel in a convoy (of pyramids iirc) around a world in Absolution Gap by Alastair Reynolds.

There was that really weird one in The Expanse that built the generation ship, Nauvoo, to spread its beliefs to the Tau Ceti. I can't remember its name, but I'm sure it will be knocking on my door sooner or latter.

Dianetics and Scientology. As PK Dick said if you want to get rich start your own religion.

The God Engines, a short novella by John Scalzi (which is unlike any other Scalzi I’ve read…). All of humanity belongs to a mono-religion that worships a god whom they know is real because that one defeated and enslaved all the other gods, who are now slave-captives serving as FTL drives aboard human starships.

The world building is excellent and the reveal/climax is one that sticks with me such that I have to re-read it every year or so just to revisit the last few pages.

In the Prince Roger series, the planet Armagh converted to Satanism.
Originally, it was settled by Catholic Christians in order to create a world where there was only One True Religion and thus no potential conflict... right up until one Preacher suggested holding Mass in English rather than Latin so that the congregation would understand it better.
The suggestion caused fractures and an outright Civil War in which the highest-ranking Churchmen ordered the establishment of a committee to preserve the religion - aka an Inquisition. This, obviously, made things much worse and finally the Armaghan Church imploded.
Those who had tried to stay out of the fight had been accused by both sides of being in league with Satan, so when the Church collapsed, it was replaced with a form of Satanism based heavily on Wicca.

In Larry Niven's Known Space, the Kzinti, a very warlike species, keep losing wars to humans. Someone decides that this must because humans really are made in the image of God. They wear human skin during rituals in order to fool God.

The Pequeninos in Pseaker for the Dead end up with a weird mix of humanist religion and Catholicism, modified to account for their unique biology.

The Eaters believed in a god and Fate. Consumption of substances generally not eaten in civilized society (bodily wastes, sand, bark, moss, bones, etc.) was seen as a way of becoming close to the fabric of Fate. This left most adherents in a state of malnutrition.

The prophet (unique among the Eaters in being obese) consumed other sentient pan-humans alive and described this as "the blessed gift of transubstantiation."

Consider Phlebas by Iain M Banks

From Terry Pratchett's Discworld: Anoia, Goddess of things that get stuck in drawers. I have words with her regularly now.

Do John Varley's ring painters count?  A group of zealots that live as nomads in orbit around Saturn and dedicate their lives to re-coloring the rings as a tribute to humanity's boundless ingenuity.  And they're locked in a brutal life-and-death war with an environmentalist faction that thinks the painters are destroying a natural wonder of the universe.

Church of Humanity Unchained from Weber’s Honor Harrington series. The doctrine of the Test, and the concept of God the Tester I find fascinating.

Raised by Wolves. The implications of what they tease out are enormous.

In the Hyperion series, how Catholicism "embraced" the cruciform parasites to form the Pax, and how they were eventually defeated.

I'm not sure if this counts but I stumbled upon a video with a debate between some Christians and some "black Israelites."

What I found very unusual was that the black Israelites follow the Bible at 100% face value. For example a common argument is that the Bible says not to mix fabrics and this mixing of fabrics is in the same passage where people try to interpret that the Bible says homosexuality is a sin. Pointing out how it's hypocritical to follow one rule but not the other.

And then Israelites said they do not mix fabrics. They interpret everything the Bible says at pure face value.

Which as far as I know simply isn't done anywhere else. The Bible has been interpreted by philosophical means since Plato as far as I know. The Bible has always been "interpreted." But these Israelite guys think you should not interpret it at all and take it at face value.

Too bad the debate was pathetic and ridiculous and done by two groups of idiots. It would be fun to see this debate over whether the Bible should be interpreted or not play out with some smart people debating.

Sort of adjacent to what you're talking about

"The Miracle-Workers" (short story) by Jack Vance is set on a lost Earth colony world where humans use "magic" in a simultaneous civil war and war against native life forms. One character begins to rediscover "real" science.

First published in Astounding (1958); it's also in The Best of Jack Vance.

The magic is definitely treated as a science. I'm not quite sure how it works except it's one of those things where people believe in it so much that it works on them because of their beliefs. Sort of like a placebo effect. Actually, it's the cleverest variation on this theme because some of the humans suspect that their magic is a false reality and want to investigate real science. Definitely worth a read if you're interested in the topic.

The Homo pupa in Derek Künsken's Quantum Evolution series. They are a human subspecies genetically modified to worship a different human subspecies. Weird as hell. Great books. Vastly underrated.

Roger Zelazny's Isle of the Dead) features a religion which appears to work. It does have physical effects but might be a sufficiently advanced technology operating offstage. In Lord of Light at least one of them remembers they're not really Hindu gods, they just adopted that schtick.

The Great God Moto.

The World of the Five Gods series by Lois Macmaster Bujold.

A couple of them come to mind:

George R. R. Martin's "The Way of Cross and Dragon", in which a priest from a far-future Catholic church goes after a heretic.

Also from Martin the religion of the vampires briefly described in the novel Fevre Dream.

The main character of Sterling Lanier's post-holocaust novel Hiero's Journey is a priest from a far-future version of the Catholic church in what is now Canada that was heavily influenced by Native American beliefs.

On a darker note there were the mutations of today's religions that appeared in "The Screwfly Solution" by Racoona Sheldon (James Tiptree Jr)

The Spirit of the Man of the Stars from David Drake's The General series was pretty interesting.

So were the Kdaptists -- Kzin who would wear skin face-masks to "look" human in an attempt to fool God so they could win against humans in a war.

War Hammer Tech Support "Have you tried lighting some incense?"

Klingon religion is interesting. Not how good you do or if you devote to prayer, just go and be the last one standing in battle.

Working on a series myself where every planet has the same thing in their holy texts. Six days of creation, a day of rest, then creation sins and gets kicked out of paradise. After that it's different. And no one can figure out how they all have the same beginnings.

Some of the adherents to The Orange Catholic Bible in Dune are way, way out there.

That there really is a loving god.

pannion domin from Malazan books of the fallen

I really like the secret societies religion from KJ Parkers 2 of Swords.

Basically they believe in "The Maker", their cult is sort of masonic, in that they dont mind you believing the maker is the sun, or god, or a chill universe or whatever. They believe that the maker doesnt make mistakes, he creates good things. But that those things might not be in the best place or being put to the correct task. So they set about recruiting, training and deploying the best and brightest to reshape the world.

Going to any further depth probably constitutes a spoiler. But its great. The way the religion shapes the story is awesome.

WorShip.
Destination: Void, The Jesus Incident, The Lazarus Effect, And The Ascension Factor. by Frank Herbert and Bill Ransom.
Complex and beautiful.

I think the Earthseed books (Parable of the Sower and Parable of the Talents by Octavia E. Butler) have an interesting take on the beginnings of a religious community. The protagonist Lauren was raised in a Christian household with a pastor for a father, but from an early age began to develop her own religious ideas, which she relies on in working to establish a new foothold for civilized society in a dystopian world plagued by crime and poverty. Her Earthseed religion doesn't center God as an object of worship or reverence, but instead conceives of God as the most powerful and inevitable force that must be reckoned with in life, and in doing so concludes that "God is change." So the focus of Earthseed's ethics is on adaptability, not resisting life's changes or despairing in the face of them but instead changing with them and doing what's needed to survive and to ensure the survival of the community through ever-shifting circumstances.

It's an impressively raw depiction of the particular spiritual mindset of someone who feels called to start a new religious movement, not as a grifter or manipulator, but as a sincere believer in the worth of her own ideas. I really wish Butler had had a chance to finish her planned trilogy. Earthseed was just taking root in the first two books, and I would have loved to see how it continued to develop in the final installment.

The Puppets in Quantum Magician. I don't want to spoil it because it's pretty crazy to read

In I, Robot - the robots in one of the stories develop a religion around beaming energy to the earth as a holy mission.

“The Word to Space ” • Winston Sanders, 1960
Project Ozma eventually pays off by detecting signals from a distant planet, but that planet is apparently ruled by theologians bent on converting the cosmos to their own dogma.

This one requires a little bit of context to get into, in the world of Halo. The covenant is a huge collective of various alien species who worship and extinct race who were much more technologically advanced. The poor belief is that the halo Ringor‘s left behind will send them on their great journey, they’re already a religious extremist group. What I found particularly interesting was a sub sect of the covenant the governors of contrition.

The halo rings were weapons meant to eliminate a parasitic zombie like infection called the flood by eliminating its food destroying all sentient life in the galaxy, the governors of contrition believed the flood was a relic left behind by the gods of the covenant and the covenant. Great journey would actually be achieved by willingly allowing the parasite to infect them. I guess it’s just fascinating to me that in an already extreme religion like the covenant you could find a secondary religion even more extreme in its beliefs.

My handle actually means "All the Gods" in Tsolyani, the conlang of MAR Barker in his Tekumel, Empire of the Petal Throne books.

In addition to languages, Barker created a very complex and lengthy set of religions for his world: https://tekumel.com/world_gods.html

There are five gods of Stability, and five gods of Change. These philosophies do NOT correspond to "good" and "evil," although they were mapped that way when TSR used Barker's Tekumel as the first setting for a D&D world back in 1976.

Each of the ten gods has a cohort god, and each cohort emphasizes one aspect of that god. So Avanathe is the goddess of Stability who oversees the crops and the seasons and also the cycles of women and the interests of women. Her cohort Dilinala emphasises "woman as woman alone," and is the goddess of specific women's interests, women's health, and lesbian women.

In addition to gods and their cohorts, every god and cohort has a seemingly-endless series of Aspects, which is the god manifesting in a particular manner, usually instantiating a particular interest of the god. For example Ksarul is the Change god of knowledge and secrets, his cohort is Gruganu, god of magical spells, but one of Ksarul's aspects is Mentutekka, the god of (secretive) forest creatures, who appears as a shade of dark blue and not in any human form, and who cares for nocturnal animals in particular.

Finally, there are demons who represent the form or substance of one or two gods. These are not gods but (often) mortal creatures, but who act in alignment with the interests of one or more gods or cohorts or aspects.

The world of the Empire of the Petal Throne game is truly a theocracy - the very first thing you have to do when generating a character is decide what deity they worship, and everything else follows from there. It's an amazingly detailed and thorough example of worldbuilding.

Perhaps not incredibly original, but I find the Mandalorian philosophy as it is described in KotOR fascinating and I wish that they had kept it in the Disney era. As I interpret it, the core of the Mandalorian creed is a sort of martial Darwinism; they seek out ever greater opponents in order to improve through the conflict (which is what precipitated the Mandalorian Wars against the Republic). This strikes me as the perfect justification for a warrior culture.