Alfava Metraxis Beach
The TARDIS lands on this beach below the crashed spaceship in episode 5x04 “The Time of Angels”.
The Doctor, Rory, and Rory's dad are teleported to the spaceships power generation room in episode 7x02 “Dinosaurs on a Spaceship”.
While waiting for information on Clara, the Doctor is staying in a monastery in episode 7x06 “The Bells of Saint John”.
Bad Wolf Bay, Norway
Rose remembers his time with the Doctor in episode 2x12 “Army of Ghosts”. Rose and the Doctor say goodbye on the beach in episode 2x13 “Doomsday”. Rose says goodbye to the Doctor once again in episode 4x13 “Journey's End”.
Rose thinks back to visiting an alien landscape with the Doctor in episode 2x12 “Army of Ghosts”.