A prisoner was an individual confined for breaking the law.
While the Chronovore Artemis was a prisoner of Mortimus, he used her powers to try to gain revenge on the Doctor. He had her alter time in various ways to destroy the Seventh Doctor. When Ace freed her, Artemis departed Earth in Mortimus' TARDIS with the aim of torturing him for her imprisonment. (PROSE: No Future)
According to one account, soon after taking office, Romana suffered an epileptic fit. During this, she signed an executive order releasing three hundred prisoners from Shada, including Grandfather Paradox. The fit was caused by the Carnival Queen threatening the rational underpinnings of the universe. (PROSE: Christmas on a Rational Planet)
Prisoner Zero escaped through a crack in time to Amy Pond's house in 1996. Years later, the Eleventh Doctor tricked it into revealing itself to the Atraxi, who took it back into custody. (TV: The Eleventh Hour)