John Paul II has never excommunicated anyone during his reign as pope. There have been people during his reign who have incurred what is called a latae sententiae or automatic excommunication, such as the radical modernist Fr. Tissa Balasuriya, who committed heresy, and the radical traditionalist Archbishop Marcel Lefebvre, who excommunicated himself by consecrating bishops without a papal mandate. Both of these offenses incur latae sententiae excommunication under canon law.
There has never been a case where John Paul II excommunicated anyone directly, but he has issued or approved notices that certain individuals, including the ones mentioned above, have themselves incurred latae sententiae excommunication by their actions.