Junkyards were places used for the disposal of waste. 76 Totter's Lane, where the First Doctor first encountered companions Ian Chesterton and Barbara Wright, was a junkyard. (TV: "An Unearthly Child") The friends later reminisced about that day, the Doctor saying, "It all started out as a mild curiosity in the junkyard, and now it's turned out to be quite a great spirit of adventure, don't you think?" (TV: "Strangers in Space")
The Doctor later stayed in a different yard, which is where the TARDIS was situated the first time he met John and Gillian. (COMIC: The Klepton Parasites)
The bubble universe that the Eleventh Doctor once landed in had a TARDIS junkyard, a home to dead TARDISes whose Time Lord masters were lured into the universe by House. The Doctor managed to reconstruct a control console using the parts. (TV: The Doctor's Wife)
The wardrobe that caused fear and panic throughout London was in a junkyard. (TV: Fear Itself)
Other references[]
Scrapyard was among the words ending in "yard" which the Sixth Doctor insultingly applied to his prosecutor, who held the title of Valeyard, during his trial aboard Space Station Zenobia. (TV: The Mysterious Planet)