The Tower of London was a prison in London. The Doctor visited it on multiple occasions and was even imprisoned there on several of them.
Henry VIII once sent the First Doctor to the Tower of London, which was where the Doctor wanted to be, as his TARDIS had also been taken there. (DW: The Sensorites)
On a separate occasion, he shared a cell with Sir Walter Raleigh. Though the event was recounted by the Third Doctor to Jo Grant, it was unclear which incarnation of the Doctor had spent time with Raleigh. (DW: The Mind of Evil) The Fifth Doctor would return to a cell there, this time with Nyssa, after falling foul of Sir Isaac Newton in the late 17th century. (BFA: Summer) Later still in his personal timeline, the Sixth Doctor and Evelyn Smythe were imprisoned there by the order of Queen Mary I in 1554, who was under the erroneous impression that they were plotting to assassinate her and place her Protestant half-sister Elizabeth on the throne. (BFA: The Marian Conspiracy)
The First Doctor assisted Lady Jane Grey and was present at her execution at the Tower (VD: The Nine-Day Queen). She was also befriended by her new lady-in-waiting Rani Chandra, a teenage girl from 2010. (SJA: Lost in Time).
While exiled to Earth, the Third Doctor once helped the Brigadier track down an alien master of disguise who had a secret base at the Tower Hill Underground station. From this base, directly under the Tower, the thief hoped to gain access to the Crown Jewels. Although a combination of the Doctor, UNIT soldiers and Beefeaters were unable to capture the thief, they did prevent him from stealing the jewels. (PHS: Secret of the Tower)
The Eleventh Doctor was once imprisoned in the Tower without trial on the personal request of King Charles II. Two days later, a sphere that was 20 feet across was seen heading away from the tower carrying the Doctor. (DW: The Impossible Astronaut)
By 2006, UNIT headquarters was located beneath the Tower of London. (DW: The Christmas Invasion) The headquarters was still used in 2009, though UNIT also maintained mobile bases in lorry trucks. (DW: The Sontaran Stratagem)
In an alternate timeline, the Eleventh Doctor was imprisoned in the Tower by Caesar Winston Churchill. (DW: The Wedding of River Song)
When The Department controlled Britain around the year 2050, the Tower of London became Dauntless Prison, a prison for all the aliens that arrived on Earth. When K9 Mark 2 and his friends released the alien prisoners there in 2050, the Department's treatment of the prisoners was leaked to the media and the prison was shut down. (K9TV: Liberation)
Sometime around the 29th century onwards, the tower was incorporated into Starship UK, its dungeon containing the devices used to torture the star whale beneath the craft into moving. (DW: The Beast Below)
