Stoning was an execution method.
In Kish, stoning was the penalty for angering the King. (PROSE: Timewyrm: Genesys)
In 54, the Pharisees ordered that Ruth be stoned for converting to Christianity. (PROSE: Byzantium!)
Stoning was adopted in the underground Marb Station on Ravolox. It was established by the Immortal and it was provided for the theft of water.
Because of a misunderstanding, the Sixth Doctor was condemned in short to stoning, but he survived the casting of stones by the excited crowd thanks to his umbrella. (TV: The Mysterious Planet)