The Doctor and Amy talk to the Queen in her rooms in episode 5x02 “The Beast Below”.
The Manor (exterior)
Clara and the Doctor visit a Manor house being haunted in episode 7x09 “Hide”.
The Rattigan Academy
Luke Rattigan runs an academy and works on his secret technology in episode 4x04 “The Sontaran Stratagem”.
Appears in 1 additional episode.
Also appears in “The Poison Sky”.
Doctor Escapes Assassins
Missy tells Clara a tale of how the Doctor escapes some invisible assassins in episode 9x02 “The Witch's Familiar”.
The Royal Collection 5145
River encounters Liz10 in a run down museum when she is stealing Van Gogh in episode 5x12 “The Pandorica Opens”.
Source: Anonymous on Tumblr