Death by Recognition

Some (usually) minor character suddenly sees someone he recognizes, but who really shouldn't be here at the moment and whose face we can't see. Then he exclaims: "You?!.." or "What are you doing here?" and gets immediately killed.

This is a much used trope, to the point of being a cliché, in British TV mystery series of the more traditional kind e.g. Midsomer Murders, Inspector Morse, anything adapted from Agatha Christie. It's a way of letting the viewer see the murder without giving away who did it.

Can become a Tear Jerker.

Related to Et Tu, Brute?.

As a Death Trope, Spoilers ahead may be unmarked. Beware.

Examples of Death by Recognition include:

Anime and Manga

In Neon Genesis Evangelion, Kaji's last words are a casual "You're late".
Happens to Kyoraku in the second Bleach movie. After a few seconds of scuffling with a mysterious ice-wielding enemy, he manages to cut off his opponent's mask and get a look at his face. He remarks "You're...!" Cue scene cut to Kyoraku in the hospital.

Comic Books

Happens to the Martian Manhunter right before Infinite Crisis (but not killed, as the main villain neded him alive).

Film

In Clue, Yvette is killed by He Who Must Not Be Seen just after saying, "It's you!"
In The Usual Suspects, Keyser Soze finds the man who can identify him, who begs him, "I promise...I told them nothing..." Soze is bathed in golden light, and then there's a Discretion Shot as Soze shoots him.
In The Man With Two Brains, Delores steps into an elevator, obviously recognizes the other occupant, smiles and says, "What are you doing here?" Then the other person (Merv Griffin) injects window cleaner into her butt. It kills her... mostly.
In Wallace & Gromit: A Matter of Loaf and Death, the opening scene is shot from the serial killer's point of view, and the confused target lets out one of these before he gets cudged on the head with a rolling pin.

Literature

In The Wheel of Time series, this was how the Forsaken Asmodean was killed. Many books later, his killer still remains a mystery:

Asmodean pulled open a small door, intending to find his way to the pantry. There should be some decent wine. One step, and he stopped, the blood draining from his face. "You? No!" The word still hung in the air when death took him.

The choir director's last words in Maskerade are "What are you doing here?
At the start of Angels & Demons Doctor Vetra sees and identifies the killer just before he dies.

Live-Action TV

First episode of Charmed started this way, when a witch said, "What are you doing here?" and then gets stabbed to death...
Lois and Clark: Elliot Gould's character says this just before he's killed by the baddie of the week, as Lois is in his bathroom and sees the killer. Subverted, though, in that we actually see the killer, too; but it turns out he's a Master of Disguise, so seeing him doesn't help. The person Lois thought she saw kill Gould was at a conference delivering a speech at the time of the murder.
Parodied on The Fresh Prince of Bel-Air. Carlton and Ashley are playing "whodunnit", and "murders" (carried out with sucker darts) of this type happen throughout the episode. Played completely straight when Will is accused of being the murderer and ends up Acquitted Too Late (to his irritation, since he isn't playing). The murderer was Aunt Vivian, if you were wondering.
The dean in Veronica Mars gives us a "What are you doing here?" The next time we see him, he's dead.
In Home and Away, Josh West says, "What are you doing here?" in the episode where he is killed. Arguably a subversion, as he had a brief conversation with the killer (later shown in flashback once he was exposed as such), before pulling out his own gun.
One (of several) fan theories about the Fade to Black ending of The Sopranos is that it's Tony having a heart attack as he sees who's entering the restaurant.

Video Games

In Metal Gear Solid 2: Sons of Liberty, Ocelot does this to a guard (he isn't hidden from the viewer, but it's a surprise that he's even there at all).
Heavy Rain. The mysterious Origami Killer visits a small-time crook in his office - a guy who had been renting space to Origami for his little 'games' in various derelict buildings. He goes, "Oh, it's just you..." and then chats a bit before the killer offs him so the victim cannot identify him to anyone.
In one of the Bad Ends of Remember 11, Kokoro manages only to say this before she is killed.

Web Comics

Parodied in Irregular Webcomic in that:
1. The victim was the author himself, and
2. The character who killed him was also the author himself, time traveled from the future to kill him.

Western Animation

In the Family Guy episode "And Then There Were Fewer", Jillian's husband, Derek, dies when he goes out to get a cell phone signal, but is cornered by the killer on a balcony.
Metallo's "Oh it's you" in Superman/Batman: Public Enemies, where after the aforementioned heroes engage him in heated battle and escape from an apparent defeat, Metallo checks the place and is approached by a shadowy figure resembling Captain Atom or Major Force. A couple of hours later, at most, Metallo's murder is pinned on Superman.