Clockwork

During his travels, the Doctor encountered various types of clockwork robots. (TV: The Mind Robber, The Girl in the Fireplace, Deep Breath, Heaven Sent, PROSE: The Clockwise Man) He also created his own clockwork robots. (TV: Under the Lake, Before the Flood, PROSE: Model Train Set)

Rose Tyler was nearly crushed by the clockworks inside Big Ben. (PROSE: The Clockwise Man)

Time-affecting clockwork technology
The prosperity of the Earth Empire depended on the Great Clock, which was largely based on clockwork technology. When Sara Kingdom broke the Great Clock to save the First Doctor and Steven Taylor in 3999, Mavic Chen, the current Guardian of the Solar System, started looking for ways to maintain the influence of the empire. (AUDIO: The Guardian of the Solar System) This eventually pushed him into an alliance with the Daleks. (TV: The Daleks' Master Plan)

Doomsday Chronometer was a device created by the Clocksmith at the behest of the Doom Coalition. This device, partially based on clockwork technology, was capable of destroying the future of the whole universe. The Eighth Doctor found one piece of it in England in 1998. (AUDIO: Absent Friends) Together with his companions and River Song, he traced the origins of the device throughout medieval Europe (AUDIO: The Eighth Piece, The Doomsday Chronometer) but was unable to prevent its completion and the destruction of the future of the universe. (AUDIO: The Crucible of Souls)

The Moment was decorated with clockwork designs. (TV: The Day of the Doctor)

Behind the scenes
The Twelfth Doctor's title sequence was heavily focused on clockwork imagery. This was inspired by Billy Hanshaw's fan sequence, and in fact Hanshaw continues to receive a credit for "title concept".