I'm not one that enjoys being herded like cattle on many of the ship offered excursions and much prefer to do it myself. There is lots of information and reviews online that document who the good tour operations are all around the world. I did my research and this is what we did on our port shops
1. Messina Sicily: my favorite stop of all, the beautiful island of Sicily. We hired Mario from SicilywithMario.com. He was absolutely fabulous, as his many reviews attest too (look him up on trip advisor). We opted to have just two of us, for a personal all day tour (200 Euros). He took us to Savoca, Castelmola and Taormina, as well as a tour of Messina and several short bonus stops. With the exception of Taormina--which is jam packed with tourist on port days--we were often by ourselves with our guide in some of the most fantastic scenery anywhere. He takes you places the tour buses cannot get to (and trust me, you don't want to drive yourself on those roads!!!). We enjoyed a fabulous lunch in Castelmola with a view of Mt Etna. This was our most expensive excursion, but well worth every penny.
2. Athens: we hired taxi driver Takis Kapoukakis and although he had a colleague show up to get us (can't remember his name)--he was very reliable. He was waiting for us as we got off the ship. Drove us to the Acropolis (pointed out land marks along the way), gave us a map with some general guidelines and agreed to meet us at the same spot at 3:00. We did our own tour of the Acropolis (there were maybe 20 people when we got there, so we basically had the place to ourselves before the tour buses arrived about an hour later). We walked around all the key sites, had lunch, finished at the Acropolis museum and then met our driver promptly at 3:00. He gave us a small tour of Piraeus on the way back. All that for a 50 Euro payment at the end--which I believe is significantly cheaper than those who negotiated for a taxi ride at the port--and much more reliable.
3. Ephesus. I felt it wasn't best to navigate Turkey on our own. We bought a tour package on viator.com which used Neon tours ($69 per person). They met us at the ship with a huge air conditioned van. Because there were just two of us, it was much easier to maneuver around all the stops. The best of Ephesus tour has the same stops as everyone else, but it was nice having a tour guide to ourselves. Stops at St Johns basilica and the Virgin Mary house were in the off times, so few people there. Unfortunately, ancient Ephesus is packed on port days, but we still enjoyed our time there. All the tours include a "free lunch" at a Turkish carpet factory. The lunch is informal but good. The carpet factory tour interesting, but a hard sales pitch at the end. I did not see a single tour that did not have that stop included, so just be prepared. We loved the apple tea in Turkey.
4.Chania Crete: don't waste your time on excursions from here, its a short stop and you want to spend it in the Chania harbor, which is spectacularly beautiful--just ride the bus from the port (constantly running on port days) right into Chania for only a few Euros. Walk the beautiful Venetian port. We took the long walk out to the lighthouse, which was well worth our time. Again, beautiful views of the harbor. I waded briefly in the water at a small sandy beach inside the seawall to the light house. We enjoyed drinks at the yacht club (near the wall to the light house) with one of the most beautiful views on the planet. Then we strolled around the beautiful town, bought a few things and ate at a place called Soulvaki Art, I believe. My lunch costs a whopping 4 euros and was absolutely delicious! The market by the bus back to the port had a small bakery with the most delicious baklava I've ever tasted. I particularly like the variety made with pistachios and drizzled with chocolate.It was a slightly chilly day or I would have tried to squeeze in a quick trip to Chrissi Akti beach (Golden beach). I could live in Chania, it was very charming. And it was by far our cheapest port day--I don't think we spent more than 25 euros on food and transportation for two people. That leaves lots of money for souvenirs on the last port call!
5. Don't forget to leave time for Rome! We spent three days before the trip and I only wished we had stayed longer. We stayed downtown in a small hotel but it was walking distance to almost everywhere.