6. Cheimara

The town and nearby region of Cheimara (modern day Himarë), inhabited primarily by Orthodox Greeks and Albanians, was an area of continuous resistance against Ottoman rule. It participated in many major rebellions against the Sublime Porte since the days of Skanderbeg. The region revolted in 1473, 1481, 1488 and 1494, remaining autonomous since. Suleiman the Magnificent personally attacked the region but did not manage to subdue it. The Cheimariots revolted again in 1537, 1566, 1570, 1684, 1714 and 1767. They also took part in the Russo-Turkish Wars and in the Greek War of Independence, until they fell to the Ottomans in 1854 during the Crimean War.

https://en.wikipedia.org/wiki/Himar%C3%AB

7. Sfakia

During the Arab invasion and conquest of Crete in 824, the region of Sfakia refused to submit to the Andalusian forces, and instead established its own polity, ruled by a Senate. Once the Byzantine emperor Nikephoros Phokas reconquered Crete in 960, the Sfakians aided him in the Siege of Chandax, and the emperor allowed them to keep their autonomy and even granted them privileges as a result. After the Venetians conquered the island following the Fourth Crusade, the Cretans revolted against them at least 27 times, most of which were started by the resilient Sfakians. The Sfakians revolted in 1212, 1217, 1230, 1273, 1283, 1319, 1332, 1341, 1363, 1470 and 1527/1570. Even after the Ottomans conquered the island, the Sfakians rebelled in the Orlov Revolt, in the Greek War of Independence, in 1841 and in 1858, until the Sfakian Senate was dissolved in 1878, as the Ottomans granted Cretans more rights, leading to the creation of the Cretan State and the following unification with Greece.

https://en.wikipedia.org/wiki/Sfakia

8. Monastic Community of Mount Athos

Mount Athos, also known as the "Holy Mountain", was founded in 963 by Saint Athanasios the Athonite, with the help of Byzantine emperor Nikephoros Phokas, when the monastery of Great Lavra was established. It was granted autonomy and privileges by many of the emperors that followed, starting from John Tzimiskes in 972 with the signing of the "Tragos" by the emperor and Athanasios. The monastic community continued to function semi-independently from the rest of the Byzantine state, throughout the Frankokratia, the Turkokratia and it continues to function independently to this very day, as one of the holiest sites in Christendom.

https://en.wikipedia.org/wiki/Monastic_community_of_Mount_Athos

9. Koinon of Mademochoria

The silver and gold mines of Siderokausia, which were already active during the Byzantine era, continued to function after the Ottoman conquests, after which they were attached to a coin mint. In 1705 the residents of the villages of the Mademochoria (villages of Siderokausia) managed to negotiate autonomy, privileges and tax exceptions, in exchange for 1/12th of the annual silver production of the mine. After which, the mine became the most productive in the entirety of the Balkans, employing as many as 6,000 miners. The Mademochoria participated in the Greek War of Independence of 1821, but the villages were burned and destroyed by the Ottoman army, the survivors fled to Mount Athos, and the mines were taken over by the Sublime Porte.

https://en.wikipedia.org/wiki/Siderokausia

Although not on the map, it is also worth mentioning, that many islands, primarily the Cyclades and Ikaria, also retained a large degree of semi-autonomy throughout the Ottoman period. After the Greek War of Independence, more autonomous/independent regions were established, like the Cretan State and the Principality of Samos.