Stoning was a method of killing individuals by throwing rocks at them until they died.
In 2268, Miramanee and Kirok were stoned by Salish after it was revealed that the latter was not a god. She died of her injuries. (TOS: "The Paradise Syndrome")
In 2370, two Volan colonists were stoned to death on the streets of Ropal City by Cardassian authorities. (DS9: "The Maquis, Part II")