Pope Julius I and a large number of western bishops were excommunicated by the eighty eastern bishops attending the Council of Philippolis in 343. The western bishops responded by excommunicating the eastern bishops.
Pope Formosus was excommunicated by Pope John VIII. He was reinstated well before he became pontiff.
Pope Nicholas I and everyone who employed the Latin rite was excommunicated by Patriarch Photias I.
Pope Honorius was declared anathema by the Council of Constantinople, but he was long dead, so he could not really be excommunicated. The bishops obviously thought that he was a heretic, but the Pope Leo II did not approve that designation.
Several popes have been deposed. Theodoric deposed Pope John I in 525 and replaced him with Felix IV. Belisarius deposed Pope Silverius in 537. Silverius was sent into exile and eventually abdicated, but not before Vigilius had been chosen to succeed him. John XII was deposed by a council of bishops in Rome in 963. A council deposed his successor, Leo VIII. The next pope, Benedict V, was deposed by the emperor. For a short while all three of them were still alive. Benedict IX resigned once, became pope again after the emperor deposed his successor, Gregory VI, and was finally deposed by Boniface, the Margrave of Tuscany. No one knows what became of Benedict.
Pope Benedict VI was deposed, incarcerated, and murdered. Franco was elected Pope Boniface VII in 974. He had to flee Rome because of pro-imperial forces. He came back and ruled again for a little while some years later. However, for some reason he is not considered a legitimate pope.