A pencil was a Human writing tool. It consisted of a center made out of graphite or other pigment surrounded by wood.
In 1996, when Captain Kathryn Janeway and Commander Chakotay encountered Captain Braxton living as a vagrant in Los Angeles, he was upset that someone had stolen his pencils. (VOY: "Future's End")
In 2152, Trip Tucker told Jonathan Archer about a teacher who accused him of stealing a pencil from her desk. He was innocent, but his mother told him to apologize anyway. (ENT: "A Night in Sickbay")
In 2266, Miri sharpened pencils at James T. Kirk's request. (TOS: "Miri")
While recovering from post-traumatic stress disorder in Vic Fontaine's holoprogram, Nog offered to look through his accounting books. He asked for a computer, to which Vic replied with a pencil, saying "It's 1962. What do you want from me?" (DS9: "It's Only a Paper Moon")