All in the Eyes

The lights dim and the character is thrown into deep shadow (or sometimes even total darkness)--except, for some reason, for a mysterious rectangle highlighting the character's eyes. Sometimes this is used to indicate intense concentration, sometimes it's used to show the character's powerful hypnotic abilities. And sometimes it's just to tell the audience, "This next part is supposed to be creepy!"

Almost never combined with Glowing Eyes of Doom. A form of Hollywood Darkness. A subtrope of Chiaroscuro.

Examples of All in the Eyes include:

Anime and Manga

Used twice in the OVA of Angel Densetsu, when the sunlight reflects from Takahise's knife into Kitano's eyes.

Comic Books

P'Gell was once drawn this way in The Spirit.

Film

The likely Trope Maker is the 1922 film Dr. Mabuse the Gambler, which features the eponymous character (a hypnotist/psychiatrist/master-criminal) in several of these sorts of shots.
As seen in the picture above, in the 1931 adaptation of Dracula, Bela Lugosi was given this close up with this effect.
- This kind of shot is used in almost every movie that Lugosi starred in.
Harry Potter and the Chamber of Secrets has this on Lucius Malfoy near the very end of the film.
Gomez and Morticia Addams display this for comic effect in the film adaptations of The Addams Family. Likely as an homage.
Le Chiffre , played by none other than Orson Welles in Casino Royale 1967.
This happens every time Lamont Cranston uses his mental powers on someone in the 1994 movie version of The Shadow with Alec Baldwin.
The slits in the window blinds at the police station create this effect on Christine Collins' face, in order to see the emotion in her eyes (and quite possibly take attention away from her lips) in the 2008 film Changeling.
The 2008 film The Haunting In Connecticut, did this to the kid in the dumbwaiter.
True Lies: Harry eyes are the only thing lit during the hotel scene. At the very end the lighting is adjusted so that Helen's eyes are highlighted like this when she gets the "Boris and Doris" phone call.
Bufford's Beach Bunnies has the Incredible Foreskin and his hypnotic abilities.
Harold Oxley has a beam of light appear around his eyes when the Soviets have Indy stare into the Crystal Skull in Indiana Jones and the Kingdom of the Crystal Skull.
Light encompasses Jack Slater's eyes right before he flashes back to his son's death in Last Action Hero.
In Highlander the camera zooms across Madison Square Garden, over the heads of the crowd, until finally settling onto MacLeod's eyes, which are lit in this fashion.
In The Blues Brothers, the eyes of Henry Gibson's Neo-Nazi leader are lit like this while he's standing in front of Wrigley Field declaring war on Jake and Elwood.
The movie version of Sin City does this, though it's not really for "spooky" reasons, but as a way of reproducing the original comic's visual look of having a character only be visible as a silhouette with only their eyes really visible.

Live Action TV

Happens surprisingly often to Captain Kirk in Star Trek: The Original Series.
In the 1996 Doctor Who Telemovie, this effect happened to the Doctor just after his regeneration scene.
Power Rangers RPM uses this effect a lot to show the Rangers talking inside their helmets when they don't want to just use a Go-onger scene with them talking.
In Supernatural, the Yellow-Eyed Demon who we later find out is named Azazel, gets a few shots like this, highlighting his - wait for it - yellow eyes.
Used extensively with "the Captain" on How I Met Your Mother

Music Videos

In the music video for Shakira's "Objection (Tango)", there is a sequence where Shakira is in the car looking for her wayward lover. Her eyes are illuminated by the reflection from her rear-view mirror.

Video Games

In the intro cutscene of BloodRayne 2, Rayne appears eyes-first in the backseat of a car.

Web Comics

Gunnerkrigg Court: The last panel here.
The Inexplicable Adventures of Bob: Galatea here, just as she Takes A Level In Bad Ass.