Time field

The Cracks were a series of splinters in the "skin of the universe," according to Prisoner Zero. The pattern of the Cracks is always the same, and the cause remains unknown. When discussing the cracks with Prisoner Zero, the Doctor stated that somebody must have opened the cracks. When he was asked if he knew what the cause was, the Doctor remained silent, signaling that he might just be at the center of the affair, perhaps through his recent arrogant meddling with the laws of time. (DW: The Eleventh Hour)

The cracks, always the same shape, began following the Doctor and Amy Pond through their travels in time and space. They later become aware of this, and Amy realises it is the same crack from her bedroom wall. The crack seemingly erased both people and events from history, causing people to never remember the removed events. (DW: The Time of Angels) Events thought to be removed include the CyberKing walking over London (DW: The Next Doctor) and the war in the Medusa Cascade. (DW: The Stolen Earth/Journey's End).

After the crack on the Byzantium disappeared, the Doctor determines that the true nature of the cracks is actually the end of the universe, heralded by an explosion, that was triggered through means as of yet unknown. It has however been hinted that this "explosion", as the Doctor put it, was caused by the opening of the mythical Pandorica. The Doctor ridiculed the references to this as of yet unexplained object or place, claiming it to be a fairytale (though River Song clearly remembers stopping the event alongside the Doctor and Amy).

List of Cracks

 * The first official crack was seen on Amy Pond's bedroom wall, which soon opened up to another area in the universe - an Atraxi prison. (DW: The Eleventh Hour)
 * The crack was seen on the TARDIS monitor, which the doctor looked at briefly before switching it off. (DW: The Eleventh Hour)
 * Another was present within the hull of the Starship UK, a space ship inhabited by the residents of the United Kingdom. (DW: The Beast Below)
 * The crack was seen in one of the Cabinet War-room(s) that the prime minister worked in during WWII . (DW: Victory of the Daleks)
 * Another crack is to be found in a wall on the inside of the Byzantium, it opens open and becomes a pure white light. When several of the Clerics go into the light, they disappear, and none of their team remember them as if they have been erased from history. It temporarily went away when it sucked up all of the Weeping Angels. (DW: Flesh and Stone)
 * Several pieces of dialogue in Flesh and Stone indicate that these are all the same crack, which is somehow following Amy and the Doctor through time and space

Behind the Scenes
The Cracks were inspired when Steven Moffatt saw a crack in the wall of his son's bedroom. Steven Moffat confirmed in the Doctor Who Confidential for Flesh and Stone that the cracks will appear in virtually all episodes (though as it was not present in Time of the Angels means that it may only appear once in the next 2 parter.