Old English stan, used of common rocks, precious gems, concretions in the body, memorial stones, from Proto-Germanic *stainaz (cf. Old Norse steinn, Danish steen, Old High German and German stein, Gothic stains), from PIE *stai- "stone," also "to thicken, stiffen" (cf. Sanskrit styayate "curdles, becomes hard;" Avestan stay- "heap;" Greek stear "fat, tallow," stia, stion "pebble;" Old Church Slavonic stena "wall").
Slang sense of "testicle" is from mid-12c. The British measure of weight (usually equal to 14 pounds) is from late 14c., originally a specific stone. Stone's throw for "a short distance" is attested from 1580s. Stone Age is from 1864. To kill two birds with one stone is first attested 1650s.