House of Calvierri (waterway & tunnels)
The Doctor and Rory row up to the mansion and make their way through the tunnels in episode 5x06 “The Vampires of Venice”.
Henry VIII's Bedroom
Amy, Rory, and the Doctor hide under Henry's bed in episode 7x04 “The Power of Three”.
UNIT Lab (exterior)
Kate Stewart escorts the Doctor and his companions into UNIT's secret research facility in episode 7x04 “The Power of Three”.
A monk comes to tells the Doctor that the phone in the TARDIS is ringing in episode 7x06 “The Bells of Saint John”.
Natty Longshoe's Castle (hall)
The Doctor plays chess against himself for control of his brain in episode 7x12 “Nightmare in Silver”.
Lucy Saxon is taken from her cell and forced to participate in the resurrection of the Master in 2009 Christmas special “The End of Time: Part One”.
Unit HQ (interior)
Clara meets joins Kate Lethbridge-Stewart and the UNIT team in investigating the trapped airplanes in episode 9x01 “The Magician's Apprentice”.
The Trap (main hall)
The Doctor eats dinner in one of the big rooms in the castle, and later watches The Veil as it pursues him in episode 9x11 “Heaven Sent”.