Pandorica

The Pandorica was a prison box, hidden under Stonehenge. It was constructed to ensure the safety of the Alliance and to hold the most feared organism in the history of the Universe, which turned out to be the Doctor.

History
It was mentioned by Prisoner Zero to the Doctor, who told him that it would open and that silence would fall. (DW: The Eleventh Hour) River Song also mentioned the Pandorica to the Doctor, telling him she would next see him there and that she remembered it well. The Doctor believed at that time that the Pandorica was a fairytale (DW: Flesh and Stone), later explaining to Amy that, according to legend, the Pandorica was the prison of a warrior or goblin who dropped out of the sky and tore your world apart until a good wizard tricked it and locked it up (DW: The Pandorica Opens).

The Pandorica turned out to be a prison, built by the Alliance for the Doctor to stop him from destroying all the universes. Their conclusions held that the Doctor would be responsible for the destruction of existence itself, and thus used the lure of the Pandorica in order to entrap him. There were many layers of security in the Pandorica including deadlocks, time stops and matter lines. It even had a restoration field to stop the Doctor from dying, which the Alliance believed to be a form of escape. (DW: The Pandorica Opens)

It was used to help save Amy Pond and she was locked inside it for 1894 years, until she was saved by her younger self, whose DNA provided the Pandorica with the material it needed to fully revive the near-death adult Amy. During this time, it was moved several times:
 * 118 A.D - Taken back to Rome under armed guard.
 * 420 A.D. - Raided by the Franks.
 * 1120 - Prized possession of the Knights Templar.
 * 1231 - Donated to the Vatican.
 * Post 1231 - Sold by Marco Polo.

At an undisclosed time it was put into storage in a London warehouse, which was destroyed by the Blitz in 1941. The box was found a short distance away, unscathed.

The Pandorica was also used by the Doctor to restore the universe. Since all of the traps inside it provided the perfect barrier against the destruction of the universe, it retained several billion atoms of the original universe within it even after the destruction of the rest of creation. Operating on the same principle as cloning a body from a single cell, these atoms provided a literal 'blueprint' for the universe when the Doctor threw it into the exploding TARDIS which cracked all of time and space. The blueprint from the Pandorica combined with the explosion energy from the TARDIS restored every point in time and the rest of the universe. Doing so also reset the timeline so the cracks never existed and all that was erased by them was restored. As the Alliance seemingly had no reason to form, it is likely it did not, and so the Pandorica likely never existed also. (DW: The Big Bang)

Exterior
The Pandorica looked much like an image of Pandora's Box found in the bedroom of Amy Pond. Since they used her memories to lure the Doctor there, the Alliance possibly designed it to look like this.

Interior
The interior was a small room with a chair in it, intending to be a prison. When someone was placed on the chair, the exterior would close, sealing them in, and many forms of security would stop the prisoner escaping.

Known prisoners
The Doctor was put in the chair by the Alliance to stop him from destroying every universe. Using the Doctor's sonic screwdriver, given to him by a future version of the Doctor, the Auton copy of Rory Williams was able to open the Pandorica and release him. (DW: The Pandorica Opens)

Though not a prisoner, Amy Pond was kept in the Pandorica by the Doctor and the Auton duplicate of Rory, after being killed. The imprisonment was meant to bring her back to life and she was restored when her seven year old self touched the box, causing it to open. Rory's duplicate guarded it from 102 AD to 1996 AD, preventing it from falling into the wrong hands and often being seen in its presence; he was dubbed "The Lone Centurion" and became the subject of myth. One of the Pandorica's powers was to keep anyone from dying as that was a form of escape. Once it got a DNA sample from the young Amy, it was able to resurrect the older one. (DW: The Big Bang)