The Library (hall & viewpoint)
Donna and the Doctor arrive at the Library and look out over the vista in episode 4x08 “Silence in the Library”. The Doctor figures out what River did with her sonic screwdriver in episode 4x09 “Forest of the Dead”.
The Doctor inadvertently saves the life of Hitler in episode 6x08 “Let's Kill Hitler”.
Hotel Adlon (entrance)
Guest at the dinner party run from the building in episode 6x08 “Let's Kill Hitler”.
Reich Chancellery (rear)
River steals a bike from some German soldiers in episode 6x08 “Let's Kill Hitler”.
The National Museum (exhibit, hallway, & roof)
Amelia Pond visits this museum with her aunt and opens the Pandorica with an older version of herself inside in episode 5x13 “The Big Bang”.
The Doctor and her companions are brought to C, the head of MI6, who tells them about the attacks on the world's spies and the potential connection to Daniel Barton in episode 12x01 “Spyfall - Part One”.