Santorini: Everyone’s favorite Greek Island. I highly recommend the towns Oia and Fira. If interested in archeology, go to Akrotiri. Unless you are diehard beach bum, skip the beaches here and save for the other port of calls. The white washed villages hanging on the cliff sides are the main draw.
Haifa, Israel: Skip Haifa and take a shore excursion to Jerusalem, Dead Sea or Sea of Galilee. Yes, it will be a long day but this is ground zero for Jewish, Christian and Muslim religions. You will only have time for the highlights, but it will still be a magical experience.
Cyprus: We only had a half day, so we opted for a shore excursion to a mountain wine making village (Omodhos) and some Greek and Roman (Kourion) ruins. The town of Limassol was a let down compared to the other ports, but there are some nice cafes and shops along the waterfront and nice beaches close by.
Crete: Fantastic! If you start/end your cruise here, plan to spend a few days if not longer. There is so much to do. At minimum, go to Knossos, Elounta/Spinalonga, Agios Nikolaos, Krista and Rethymno. Heraklion has excellent cafes and top rated museums. Rental cars are reasonable and there is a good highway that runs along the North shore to all the above mentioned places. Several nice tourist developed beach resorts lie along this region. There are great restaurants in all the places, good markets and wine tasting.