Nuns Are Spooky

They have the skirts too of course, so many skirts and veils that you could never hear or see their feet. "Hover Nuns" we used to call them. [...] They're damn spooky.

—John Rodgers, on his time in a Catholic School.

Nuns follow a spiritual calling, and the word "ghostly" used to be a synonym for "spiritual" (see, for example, Ivanhoe by Sir Walter Scott, and the King James Bible which refers to the Holy Ghost), so maybe this is why nuns in movies are sometimes otherwordly, and seem touched by the supernatural in ways that are frankly disturbing. Other times it's more that the nun's reason for having become one is less about being 'called' than a try at redemption or willing away some horrible trauma in the past.

There is an exception, of course, for when Nuns Are Mikos. Contrast Naughty Nuns. Compare and contrast Nuns Are Funny and Nun-Too-Holy. For when they're actually villains see Sinister Minister.

Examples of Nuns Are Spooky include:

Comic Books

Warren Ellis's Fell features a recurring character that is a crazy nun wearing a Nixon Mask. Ben Templesmith's artwork certainly works well for the spooky factor.

Fan Fiction

Mostly averted in The Teraverse's Sister Marie. She's actually pretty down-to-earth for a (telekinetic) flying nun, most of the time. But in one memorable scene, she lost her temper and exited a press conference by flying into her church, the doors of which seemingly opened for her on their own. And on another occasion, she intervenes in a possible suicide-jumper situation by introducing herself while nonchalantly hovering in midair directly in front of the prospective jumper.

Film

The Blues Brothers: The Penguin (With the extremely-intimidating name of Mother Stigmata) does not walk, she glides. Doors open and close without her touching them. Of course, this is all Played for Laughs and is likely a Lampshade Hanging of this trope.
The Omen: The nun at the hospital seems quite sinister, as she tells Gregory Peck that she can't give him any information. She then rises silently up the paternoster lift. Paternosters had been discontinued long before the film, and there was no reason to have one in a hospital that had been recently refurbished, except that getting into a common-or-garden elevator and waiting for the doors to close wouldn't look as spooky.
- However, this paternoster doesexist, and in an hospital to boot : The Northwick Park Hospital, Harrow, Middlesex. This is an example of Truth in Television.
- Presumably Nuns have to 'pater noster' several times a day.
  - According to the DVD commentary, the paternoster used in the film just happened to be in the shooting location and it was in working order.
In Alfred Hitchcock's Vertigo, the gliding dark spectre which prompts Kim Novak to jump to her death turns out to be—a spooky nun.
The dwarfish nun from Federico Fellini's Amarcord. We never see her face or hear her voice.
In one of the Nightmare On Elm Street films, Freddy's story is told by a spooky nun who, it is suggested, is the ghost of his mother.
The black comedy film Death Becomes Her has three. Bruce Willis meets the trio at a hallway leading to a morgue. Like Penguin, they do not walk, they glide. Ghostly sobbing for added creepiness.
Spy Hard has gun-toting nuns.
Invoked in The Town, where the bank robbers wear creepy nun masks and habits during one of their "jobs".
The supernatural horror film The Nun.
When the evil alien first appears in Species: The Awakening, she's disguised as a nun.

Literature

The Armchair Thriller Quiet As a Nun played upon the quietness of a nunnery and The Faceless appearance of nuns as a form of horror.
Parodied with the Satanic nuns of the Chattering Order of Saint Beryl from Good Omens, who are only scary if you have a phobia of little old ladies who don't know when to shut up. (Who doesn't?!)
In Victor Hugo's Les Misérables, the hero escapes Inspector Javert, in one memorably spooky scene, by ducking into a small monastery in Paris, and immediately is convinced the place is haunted as he witnesses the self-flagellating rituals of the resident nuns.

Live Action TV

Parodied in Four on the Floor, with the videogame spoof "Karate Nuns".
Subverted in Call the Midwife, Jenny is a bit freaked out when she first arrives, the nuns are very nice and ordinary.

Tabletop Games

Another parody: Ground Zero Games' "Nuns with Guns" miniatures, which are what the name suggests.
Similar to the above example, but played straight: Warhammer 40,000's Adeptas Sororitas, a religious order dedicated to kicking ass, taking names, and setting the bad guys on fire.

Video Games

In Chrono Trigger, the nuns in the church of the past appear to be creepy, but this is later shown to be because they are secretly all Nagas.
Painkiller has demon nun enemies.
The battlenuns in Brutal Legend managed to prove that this trope and its opposite are NOT mutually exclusive.
In Tales of Monkey Island Chapter 3: Lair of the Leviathan, there is a picture of Sister Agnes, a nun with a creepy face, which is what Noogie is afraid of.
Double from Skullgirls usually takes the appearance of a nun, but her true form...

Webcomics

And yet another parody, sort of - the Satanist, gas-mask wearing "Little Sisters of Belial" in Scary Go Round.
There's something a little off about Sister Edith in Silent Hill: Promise.