Physical Religion

So let us assume we have a Crystal Dragon Jesus cult which worships a certain god. Except it's not your standard, realistic religion, which relies on belief and hope.

There is a Physical God, everyone knows there is one, everyone's belief is out of question - not believing in God is like not believing in your neighbors. More than that: the fact that it exists is the reason the religion has been started in the first place! And yet there is a religion that worships it - there is less mysticism and theology and more requests and glorifications.

You should note that this doesn't always have to have a deity be the physical aspect. A Sentient Cosmic Force or other physically certifiable religious paths may also be used. It's just the most used.

If someone still refuses to believe in God, he's a Flat Earth Atheist. If someone is not a member of this church, he is a Nay Theist. Compare Religion Is Right, where the religion came first, then the entity believed in is proven to be true. Gods Need Prayer Badly is rather common. If Religion Is Magic, then God will grant spells those who worship him. He may say Stop Worshipping Me!! if he is bugged with that, though. A God-Emperor usually has both a Physical Religion and openly rules his worshipers, making for a "real" theocracy.

Subversions occur when someone falsely claims to be a deity for whatever reasons and gets a religion.

Anime & Manga

 * The Sage of Six Paths from Naruto fits this description, as his religion was jutsu, something that all ninja can do; except that he could do it better than anyone else, which is why they worshipped him. Surprisingly, Nagato also has a Religion in which followers pray to him because of his god-like strength and Dōjutsu. It seems as though all people with the Rinnegan are hailed as Physical Gods.
 * The Saint Church of the Lyrical Nanoha franchise is based on the worship of Olivie Segbrecht, the last Sankt Kaiser of Ancient Belka, who was instrumental at finally ending the Ancient Belka War. While parts of her life are under debate, her existence and what she did are not.

Comic Books

 * The DCU - particularly the likes of Lucifer, Hellblazer and The Sandman. Gods are quite real... and they might be waiting to cause hell for the protagonist - or, just to peacefully chat. Whichever.
 * There are many real gods in the DCU outside of Vertigo-based series. For example, the New Gods are quite prominent ones, most notably Darkseid for Darkseid Is.
 * In one Thor storyline, humans started worshiping Thor as a god, even declaring themselves the true religion since, well, Thor IS a god and you can actually SEE Thor in action.

Film

 * While it's not a deity, and there isn't worship involved, the Force is very real.

Literature
"Dionysus: "Well of course they stopped worshiping us, we went to Everworld. How can you expect people to worship a god they can't see from time to time?""
 * Discworld utilizes this trope, as there are gods, religions worshipping these gods, Nay Theists, Flat Earth Atheists, and cults worshiping gods that are MIA.
 * The cults of the Old Gods and later, the Lightbringers from Arcia Chronicles worshiped the respective Physical Gods until they were killed or abandoned Tarra. The modern predominant religion is basically a fantasy counterpart of Christianity (minus Christ).
 * In the Heralds of Valdemar, the Tayledras, Shin'a'in and K'Leshya, collectively known as the Kaled'a'in, are called as such because they worship the Star-eyed goddess Kal'enel, who routinely provides divine intervention of the kind that cannot be mistaken for anything else, as well as being able to communicate with her devotees in 'the moonpaths'. Also in the Valdemas world is the god Vkandis, worshiped by the Karsites  who actually sent a lightening bolt to vaporize a false Son of the Sun (like their pope) who wasn't abiding by his doctrines, choosing a new one himself through a statue of him, even going so far as to prove it wasn't a trick by removing the crown which was a permanent, non-removable part of the statue and placing it on the new Son of the Sun and putting the statue back, crownless.
 * In one of the Everworld books, Dionysus is unsurprised to learn that the Greek gods are no longer worshiped in the "Old World" (our world).


 * This is much to the amusement of real worlder Jalil.
 * The Sandworms, or Shai-Hulud, from the Dune Universe are this.
 * David Eddings tends to rely on this trope for his plots. The Belgariad universe has eight gods and two godlike consciousnesses of the universe, and The Elenium has more deities than anyone can count.
 * Regarding The Wheel of Time, Robert Jordan has used the following quote to explain the lack of organized religion: "This is a world where what might be called the proofs of religion are self-evident all the time. It seemed to me there was no necessity for the trappings of religion, which by and large are to reinforce us in our faith and to convince others. If your beliefs are made concrete and manifest around you at any given time there is not the need for that".
 * Philip K. Dick's A Maze of Death features such a religion.
 * Lois McMaster Bujold's Chalion series, with its four or five Gods, depending on which sect you belong to. (There is no doubt about the existence of the Bastard, the fifth God. The argument is over whether or not he should be ranked up with the other four.)
 * The Valar for the peoples of Middle Earth: the Elves are on first-name basis with them. The Númenoreans don't have any organized religion either, until Sauron introduces it for his own purposes.
 * They at least have a vague religion dedicated to Eru Ilúvatar, but arguably the fact that He's not immediately present explains their rebellion.

Live Action TV

 * Deep Space Nine shows us the Prophets, incorporeal beings that exist outside of linear time, worshiped by the Bajorans. Several times in the series, Bajoran prophecies are brought up but doubted by skeptical characters while others (who may not even worship the Prophets) will point out that these prophecies have a way of coming true (just not always the way people expect them to, being written in metaphor and imagery) because the wormhole aliens/Prophets really do exist outside linear time and thus see the past, present, and future all at once (to the point of knowing what can be changed and what can't and what the consequences will be).
 * This is all over the place in the Stargate verse. The Goa'uld are worshiped by human slaves all over the galaxy, and the Asgard have been deified by a few Nordic cultures.
 * And don't forget the Ori, perhaps the best example of all in light of their proximity to genuine omnipotence.

Mythology and Religion

 * It can be safe to say that every single mythology accepts this as a premise.

Tabletop Games

 * Warhammer / Warhammer 40000's Chaos gods. They exist, show up in person, and give gifts to people.
 * Also from Warhammer: Sigmar, god of The Empire's religion.
 * Warhammer 40000: the God-Emperor of Mankind (though his actual divinity depends on who you're talking to: the Imperium and some Space Marine chapters believe he is; Eldar, Traitor Legions and some chapters don't (though they view him as the ultimate man)).
 * Dungeons and Dragons has a large pantheon of gods, and nobody really questions their existence, seeing as they, again, show up in person and grant spells. Except for Ao in Forgotten Realms, who is so powerful he doesn't care.
 * In the setting of Eberron, the Physical God trope is averted. The true gods, if they exist, do not manifest themselves physically. There are tales of them doing it, but that's nothing more that myths and legends. However this trope still applies, as faith powers divine magic, so someone believing in the divinity of a mortal can still have divine magic. This leads to certain mortal beings having become the "God" of their churches.
 * The Lord of Blades is the Warforged Messiah of The Blades, who worship him as a divine entity. His teachings are how Warforged are a superior race and fit to inherit the world.
 * The Lich Vol is the holy figure of The Blood of Vol, a religion that preaches immortality through undeath and defiance against the "gods" who hoard the immortality. Vol herself only regards her religion as a tool for her plans to Take Over the World.
 * The Lizard Folk of Q'Barra worship the Dragon Rhashaak, who rules over them as a god.
 * The Church of the Silver Flame worships the titular Silver Flame, a cosmic force of good manifested in a pillar of fire in their capital city, the location of a battle between a Couatl, a Demon Lord and a Paladin. This particular pillar has the mind of all three beings composing it, but it's worth mentioning that the Silver Flame itself is a cosmic force not limited to that single pillar; a left over of the spell cast by the Couatl to seal the Demons in Khyber.
 * In Exalted, most religions are like this. However, the more powerful the god worshipped is, the less likely it is to show up in person - the Celestial Gods are addicted to the Games of Divinity, the Elemental Dragons are asleep, and the Yozis are Sealed Evil in a Can.

Video Games

 * Warcraft has something that's not a religion but a philosophy: Path of Light - it grants spells. Night Elves worship Elune, who most certainly exists as well. Draenei have a sort of a cult dedicated to Naaru. Dragons are kind of godlike as well, and they give quests in Wyrmrest Accord. Not sure whether people worship Titans, but they most certainly existed.
 * In Harvest Moon people worship Goddess of Harvest. Not only is she very real: you can screw her.
 * Arcanum gives us interesting example. Most mainstream religion in a world is worshiping a powerful elven wizard called Nasrudin, who lived long ago. They got most of the events right, except the fact that
 * The three golden goddesses and various other deities of the Zelda universe.
 * The entire Greek pantheon is real in God of War.
 * Touhou Project has a pair of goddesses (and their Shrine Maiden) who are trying to spread their worship in the mystical land of Gensokyo because Gods Need Prayer Badly. Backstory also shows that several other Shinto gods also existed.

Western Animation

 * Primus and Unicron in the various Transformers 'verses.
 * South Park has Jesus living in town in the early seasons and hosting a talk show. In one episode, Jimbo prays to Him for the local team to win, to which Jesus, who is sitting a few rows down, tells him to leave Him alone.
 * In Family Guy God and Jesus will sometimes show up in earlier episodes. This only makes the "religion is stupid" messages in latter episodes all the stupider.
 * Averted so far in My Little Pony Friendship Is Magic with the royal princesses. Celestia and Luna raise the sun and the moon respectively and ponies are rather prone to falling all over themselves in awe (and/or terror) when either shows up in person -- yet as of the end of season 2, no such thing as an actual formal pony religion has yet been shown to even exist.
 * They do, on the other hand, have expressions like "Thank Celestia!", "In the name of Celestia!" and "As Celestia as my witness...".