This reprint of an article in Ami Magazine gives a brief introduction to Israeli excavations of ancient synagogues.
PaleoJudaica has posts on most of those mentioned. Start at the links and keep going from there: Zodiac synagogue mosaics at Beit Alfa and elsewhere, Masada, Magdala Synagogues and Stone, Hamat Tiberias (Hamat Teveryah), Katzrin, Huqoq, and Umm el-Kanatir.
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