Creepy Cathedral

So, you're up against the Corrupt Church. You know that they're lying to the people, but no one will listen to you. It's time to take matters into your own hands, storm their base and reveal them for the evil bastards they are.

There's just one little problem. That means you actually have to go in their Church. And that place is scary as Hell itself.

The Creepy Cathedral might not have the oomph of a good old Haunted Castle, and it might not seem to give off that scary dungeon aura...but there's just something about it that makes you think, "Oh Crap!", the moment you go inside.

Bonus points if it's accompanied by organ music. Triple Word Score if it has Ominous Latin Chanting. May have spooky nuns and Creepy Cool Crosses at no extra charge.

Action Adventure

 * Most Castlevania games hold a "Chapel" level. Circle of the Moon had one with a giant lamb's head that spews poison, fireballs and flying skulls, while Curse of Darkness has an extra-boss living inside a mass of corpses, hidden in the church, in a room full of bodies that make the walls. (Scares and Womb Level, anyone?)
 * Aquaria has the Mithalas Cathedral which takes this Up to Eleven and combines it with Womb Level: it's got Shoggoth-like monsters, Meat Moss everywhere (plus tentacles), worm enemies coming out of the walls, mutants that look too much like Naija for comfort, and you have to at the end. Do not play this level if you are planning to get any sleep that night.

Fighting Game

 * The "Antares" stage in Tekken 5 is a dimly-lit, mostly red colored cathedral. The same stage reappears in Tekken 5: Dark Resurrection, although the creepiness is gone; it's well-lit, snow pours in through a hole in the ceiling, and the music is miles ahead of its predecessor.

First Person Shooter

 * In the FPS video game Painkiller, one of the early stages is exactly like this. You fight your way through a graveyard full of revenants and confront the Big Baddie inside the cathedral. Something about the place isn't quite right... maybe it's the dismembered corpses suspended by chains from the ceiling?

Hack and Slash

 * The Chaos Sanctuary in Diablo II looks like a cathedral. The problem is, it's in hell and it doubles as Diablo's home. When all five seals are opened, the place glows red.

Roguelike

 * Dwarf Fortress players tend to favor these as megaprojects, after Evil Towers Of Ominousness of course. They usually to revolve around offerings of blood for the blood god, Armok.

Role Playing Game

 * The Hulle Granz Cathedral from the .hack//G.U. games. Might not have the whole dungeon thing going, but makes up for it with sheer imposing ominousness, as well as being the home to more than a couple plot twists and epic battles through the series.
 * The cathedral in Chrono Trigger has the whole "totally not evil" shtick going on, even though the residents couldn't be more obviously evil.
 * Tales of Phantasia had the Cathedral of Fenrir. With, for bonus points, an organ BGM named "Perverse Religion".
 * The Big Bad of Fallout 1 resided under a Cathedral in the ruins of Los Angeles. The basement levels are especially creepy.
 * Creepy Steeple from Paper Mario the Thousand Year Door.
 * The main feature of the Undead Parish in Dark Souls. With plenty of tough Undead, some very troublesome unique foes, its bell tower is also home to the first Bell Of Awakening.

Stealth Based Game

 * Thief: The Dark Project has a level where Garret must infiltrate a Hammerite cathedral at the epicenter of a disaster that ruined a district of The City decades ago, which has now been walled off and is infested with The Undead. The in the cathedral itself are especially dangerous, and it is one of the most chilling levels in the game. The Soulforge Cathedral of the Mechanists from the second game (Thief : The Metal Age) isn't haunted, but it's still a very eerie place to be (at least during the events the mission is set in).

Survival Horror

 * Oublie Cathedral from Eternal Darkness would qualify. Most of the fighting and exposition takes place in the catacombs beneath it, though.
 * The final level of Silent Hill 3 rakes place in the cult's church, which in complete with pews, pulpit, and confessional.
 * The one in Brennenburg castle from Amnesia the Dark Descent fits the trope well.

Comics

 * The Ossuary of Orqwith in Doom Patrol.

Literature

 * Poul Anderson, Operation Chaos. The cathedral and surrounding town of Siloam are extra creepy, including nonstop chanting of Barbarous Names.
 * Most buildings are creepy in The Monk, but cathedrals, monestaries, and nunneries take the cake for places of of incredible terror and torture.

Web Comics

 * Silent Hill Promise: St. Stella Church

Western Animation

 * The Cathedral, a highly creepy CGI short by Tomasz Bagiński.