The Harlem Shake was originally a dance from 2001 based on rigorous shoulder movements demonstrated in Eve's video for her song 'Who's That Girl.' The video below shows a brief clip demonstrating the dance.
On May 22, 2012 a producer named Baauer who produces trap and bass music released a song called 'Harlem Shake.'
On January 30, 2013 a vlogger named Filty Frank came up with a compilation video of comedy sketches, the first of which was this video. (Harlem Shake is first 36 seconds.)
On February 2, 2012 some kids under the Youtube name SunnyCoastSkate posted the video (CLICK HERE FOR THE ARTICLE!) whose style seems to have become the most commonly used.
Since then the Harlem Shake meme has caught fire so hard it's difficult to keep up with all the new versions. Some examples:
AND, OF COURSE, OUR VIDEO FROM THE THE 21 PILOTS SHOW DONE BY NEW POLITICS AND 94.1 LISTENERS!!!!
Some say the origin of the Harlem Shake really came from the Norwegian Humping Men.(CLICK HERE FOR NSFW VIDEO)
There is, however, no proof to support that.