Graphite was the principal material within a standard HB pencil. The scribble creature that Chloe Webber, under the influence of the Isolus, created by animating a scribble on paper with ionic energy, which attacked Rose Tyler in London in 2012, was made of graphite, as the Tenth Doctor demonstrated by rubbing some of it out with an ordinary rubber. (TV: Fear Her)
Graphite could also act as a conductive material for the Doctor's sonic screwdriver's power. The Fifth Doctor once used a pencil in that manner to short-circuit androids. (TV: Four to Doomsday)
According to Rose Tyler, the Doctor's familiar scent was a mixture of graphite, lime, and diesel. (PROSE: The Turning of the Tide)
Behind the scenes
Graphite is a crystalline form of carbon, much like diamond, as well as a form of coal.