A prisoner was an individual confined against their will by another party.
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 II 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)
At the onset of the Thal-Dalek battle, the Daleks took the First Doctor, Susan Foreman, Ian Chesterton and Barbara Wright prisoner. The four initially managed to escape but the Doctor and Susan were soon recaptured and restrained within the Master Room, not freed until the Daleks had been defeated. (TV: The Daleks) Fifty cycles later, when the revived Daleks attacked the Thal City, the Dalek Supreme ordered no prisoners to be taken, save for the Doctor from whom they intended to extract the secrets of the TARDIS, and Susan, whose safety they intended to use to blackmail the Doctor into cooperating. (AUDIO: Return to Skaro) During the Dalek-Movellan War, when the Daleks sought out Davros, they used their prisoners as a labor force. (TV: Destiny of the Daleks) During the Last Great Time War, the Daleks used their prisoners as power sources, (TV: Dalek) or test subjects for their experiments. (PROSE: Engines of War) Both the Dalek Empire, (TV: Destiny of the Daleks) and the New Dalek Paradigm operated camps of prisoners. (TV: Asylum of the Daleks)
After Missy had stolen a piece of his TARDIS, the Monk sought revenge and imprisoned her on his space station. She quickly freed herself only for both Time Lords to be abducted by the Ogrons and held prisoner on their homeworld. (AUDIO: Too Many Masters)