The universe is a big place, and time is infinite. Of course, the Doctor's going to visit some places more often than others, but it's somewhat surprising how often the Doctor lands somewhere that could remind him of Bad Wolf Bay (the beach in 'The Time of Angels', the engine room in 'Dinosaurs on a Spaceship'). In 'Planet of the Ood', it's noted that the Ood Sphere is in the same star system as the Sense Sphere, a planet the First Doctor encountered in The Sensorities, and the Harvesters from 'The Doctor, The Widow and the Wardrobe' are from Androzani Major, last visited in The Caves of Androzani. The moon-like surroundings of 'Nightmare in Silver' are a reference to fellow Cyberman story, The Moonbase, and the chess-playing Cyberman from 'Nightmare in Silver' is referred to as the "699th Wonder of the Universe", a reference to there only being that many after the destruction of the City of Exxilon. The Silver Devastation was home to both Professor Yana and the Face of Boe, and when the Doctor mentioned "universes where the laws of physics were devised by the mind of a mad man" ('The Rings of Akhaten'), he could've been referring to Omega (The Three Doctors). Maybe the subtlest setting reference though is that Area 51, in 'The Wedding of River Song', was situated in a pyramid: is this a nod to the Great Cobalt Pyramid being built on the ruins of the Torchwood Institute, or just a coincidence? And on the subject of times and spaces, have you ever noticed how often the Doctor visits the 51st Century? 'The Girl in the Fireplace', 'Silence in the Library' and 'The Time of Angels' are all set there, and it's the century that Jack Harkness was born.