They go by Emperors of Japan. Showa was the Emperor during the first run of films, Heisei was the Emperor during the second run. Though they do run over each other (Showa was still there during GODZILLA '85, but that movie ties in with the following films, so it gets labeled as a "Heisei"). I believe this was done just to seperate the series. The last group are known as the Millenium series, for the obvious reason.