Ominous Mundanity

Basically, when a perfectly mundane or simplistic name is used for dramatic and sinister effect. When the writers don't want to invoke Doomy Dooms of Doom, this makes a nice substitute. Something about a realistic name brings the plot closer to home and if done properly, is scarier than Spiky Cliffs of Evil Soul-Crushing Damnation. (Often, if the name is taken out of context, it wouldn't sound scary at all.)

This trope is also the reason you ought to watch out for anyone named "John Smith". Unless he has a blue box. Especially if he has a blue box.

Film

 * In The Matrix, the Agents all have extremely common names, including Brown and Smith. The good guys, on the other hand, have Faux-symbolic handles like Neo, Trinity, Morpheus, etc.
 * Jonathan Doe in Se7en
 * District 9.
 * Monty Python and the Holy Grail. You, there! Sinister-looking warlock! What is your name? "There are some who call me... 'Tim.'"

Literature

 * Room 101 in George Orwell's Nineteen Eighty-Four.
 * In Carpe Jugulum, all the cool vampires opt for mundane names, and one vampire mentions that the witch Agnes (Agnes actually is her real name) is wonderfully clever for coming up with her name.
 * This is less for ominous effect than comedy, inverting people's attempts to give themselves cooler names (especially if they're into vampires and the like.)
 * Particularly apt, since Agnes Nitt's pseudonym of Perdita X. Dream ("The X stands for 'someone with a really cool and interesting middle name'") used to be the Trope Namer for Awesome McCoolname.

Live-Action TV

 * In the HBO series True Blood, one of the main characters is a vampire named Bill Compton, and Sookie is surprised that he has such a boring name.
 * In the TV series American Gothic, Sarah Vowell chooses the Goth name 'Becky' because it is the scariest name she can think of.
 * Criminal Minds does this with some episode names: "Jones", "Lucky", "Mosley Lane", etc.

Video Games

 * Half Life: City 17.
 * The Resident Evil series sees The End of the World as We Know It, courtesy of the Umbrella Corporation.

Visual Novels

 * Higurashi no Naku Koro ni translates to 'When the Cicadas Cry', which essentially holds the implication of 'in a hot summer day', while still holding a vague hint of menace, since the Japanese word 'naku' has the same double meaning as the English 'cry'. Unfortunately the English translation went with much more unambigiously creepy title, When They Cry.

Real Life

 * Area 51.
 * The Manhattan Project, the development of the most devastatingly powerful class of weaponry the world has ever seen.