Light and darkness play an important role in every religion. When it comes to Christianity, however, Catholicism is by far the most associated with dark elements, including exorcisms, evil hidden behind a collar or more mundane ones like corruption and a very controversial history (which, however, isn't uncommon when it comes to religion). Unless these things are portrayed as literal light, in which case it's all light.
Creepy Catholicism embraces the description of Catholicism either as simply uncanny and dark or outright criminal and corrupt, especially if compared with other religions. This portrayal is typical of countries characterized by a Protestant majority. Once the Protestant Reformation got going, many Catholic traditions were suppressed. The sort of very bloody and gory art (crucifixes, frescoes of martyred saints, etc.) and ostentatious church decor popular among Italian, Spanish and Latin American Catholics, for example, can be quite shocking to someone from one of the more austere Protestant sects that favor plain wooden crosses and unadorned churches.
So if a writer wants to evoke the sort of mood and creepy factor of a pagan sacrifice or incomprehensible witch-doctor ritual, yet make it Christian, then the creepier sort of Catholicism is the way to go, especially once you toss in some Ominous Latin Chanting.
Truth in Television much of the time, since Catholicism retains many of the "otherworldly" traditions discarded by Protestant churches (the aforementioned Latin chanting, exorcisms, Purgatory, transubstantiation), some of which might seem like something straight out of a horror film to non-Catholics, especially children. That isn't to say that certain Protestants don't also have some spooky beliefs and rituals (snake-handling, the Rapture, etc.). And of course, more knowledgeable Catholics might point to Orthodox Christianity as being even spookier: besides keeping the same beliefsnote and medieval trappings—and then some—you think the chanting is ominous when it's in Latin? Try it in archaic Greek, or Syriac, or Old Slavonic, or Coptic (which is Ancient Egyptian with some Greek tossed in), plus people prostrating themselves and hermits going into really weird kinds of meditation. Catholics in general were historically also more open to science and magic (relatively, of course; one can list many heresy cases for either, after all), having an extensive number of scientists and alchemists under its name, so it is a lot easier to demonize Catholicism as demonic or "false Christian" than other Christian groups, which often tend to reject science and/or magic.
Creepy Cathedral and Hollywood Exorcism are generally associated with this trope. If a Pedophile Priest or a Sinister Minister appears, he'll probably be Catholic (but not always). May have something to do with Christianity Is Catholic. Anime Catholicism may overlap with this trope.
- From Black Lagoon, "The Church of Violence" run with an iron fist by Sister Yolanda, an (apparently) elderly nun who wears an eyepatch and a fully - loaded, custom Desert Eagle pistol under her habit at all times. The church is not actually an official subsidiary of the Catholic Church, it's a cover for a gunrunning operation that is funded by the CIA.
- Blue Exorcist, where Satan is the Big Bad and The Vatican are supposed to be the Big Good. The main characters (one of which is a child of Satan ) are studying at a school for exorcists to learn how to fight demons.
- The Vatican in Hellsing is portrayed as a rather dangerously fanatical organization with a violent hatred of Protestants and other non-believers. They are technically a force for good, since they fight against monsters and vampires as well, but their Knight Templar actions in the series make them secondary antagonists.
- Nightcrawler from X-Men is a devout Catholic, but his demonic appearance is seen as scary by many, and he has an affinity for shadows, which emphasize the "dark" elements of his character. On the other hand, he had a cheerful and nice personality. The film version plays this trope straighter, by giving him a more introverted personality and self-inflicted scars as a way to atone for his sins.
- The Exorcist and every other movie dealing with Christian exorcism. Interestingly, The Exorcist had a Jesuit priest and teacher as a technical advisor (he also played the part of Father Dyer). The priest stressed that the Catholic Church typically doesn't condone exorcisms anymore and it is something of an Old Shame within the church.
- Constantine. Several of the characters fighting against demonic incursions are Catholics, one of whom is a priest (Father Hennessy). The title character uses Catholic rites against demons, including exorcism and the Last Rites, and is definitively an Anti-Hero.
- In The Blues Brothers, the title characters go "to see 'The Penguin'" - who turns out to be not the Batman character, but a very stern, heavyset, intimidating Catholic nun who wields a wooden 1-foot ruler like a martial arts weapon and moves with a Ghostly Glide.
- The Nun is basically this trope if it were made into a movie.
- Angels & Demons: Religious buildings in Vatican City are used as locations for the murders. Also, the description of the papal conclave wouldn't be out of place in a locked room mystery.
- The Da Vinci Code: Features the Evil Albino, self-mutilating monk Silas, a member of a heavily fictionalized version of the Catholic Opus Dei organization and one of the main antagonists. Silas himself is definitely meant to exude creepy, but Opus Dei itself is characterized as a sinister secret society in service to the Pope and a part of an Ancient Conspiracy. As you can imagine, this portrayal rather annoyed the Real Life Opus Dei organization.
- Through extensive and chillingly visceral Crystal Dragon Jesus, Magic: The Gathering has made an art out of portraying fantasy Catholicism as corrupt and fanatical. And, naturally, always white-aligned (except for a few examples dabbling with black-magic).
- In Dominaria, the old Church of Tal had elements of medieval Catholicism, both aesthetic (Templar-like knights, black-wearing priests, witchunters) and philosophical (witchunting, taking specific literature as key above all other forms of religious expression). A religious institution devoted to purging ther world of magic, they were revealed to be hypocrites using White Magic spells, and lost their political power.
- Ravnica's Orzhov Syndicate is very blatantly ripped off visually from the catholic church, and holds a similar hierarchy (aside from a pope). They promise salvation to the people of Ravnica, but are essentially a mafia group under a holy façade.
- Ixalan's Church of Dusk lifts from historical conquistadores and their fanatical religious obsession. Combined with being literal vampires, it's not hard to see the commentary on Catholicism from that era.
- Brave New World supplement Covenant. The Catholic Church has a secret group of heroes with super powers that fight against demonic influence and other supernatural monsters.
- Many of Warhammer 40,000's more outlandish religious elements (concerning the Imperial creed, the Dark Gods are something else entirely) are Flanderized elements of Catholicism: everyone wears hooded robes, exorcisms are a necessity (one Space Marine chapter even uses it as part of their inititation), pipe organs are mounted on tank treads to provide inspiring hymns and missile support... old canon even implied the Emperor was Jesus and Saint George in one of his many "guide humanity towards betterment" disguises, new canon only kept Saint George (replacing the dragon with the C'tan star vampire called the Void Dragon and killing it with locking it up on Mars).
- There are many memes in which Benedict XVI is compared to Senator Palpatine.
- The Simpsons: The episode "The Father, the Son, and the Holy Guest Star" has Bart sent to a Catholic school, where great emphasis is put on martyrdom and suffering.