Excursions from Samos to the impressive archeological site of Efese, Turkey are sold by local travel agents. If you are interested in archology, it's a must-do. I would have preferred to go there "non-organized" but as you need a visa to enter Turkey (being a non EEC country).
I chose to book an excursion (with of course the usual trip to a pre-booked restaurant and carpet-seller); the agency takes care of the visa for you. Usually you have to leave you passport with the port authorities (don't worry, you WILL get it back) in order to make the "visa-thing" go smoother. Possibly by now the agencies sell "boat +visa only" trips now; you will have more time -and you will need it- to see all of its beauty. From Kusadasi port it is a short bustrip to Efese. Try to see Efese before or after June/July/August because it is TOO hot and TOO crowded.
If staying on the south coast of Samos, in or near Pythagorio, make sure you day-trip out to this island.
Samos doesn't have that many good beaches, but out here there is one. It is quite popular with visiting sailing boats and sightseeing boats, but only the owner of the islands's family has the privilege to fully use the island.
On the ridgetop above the little bay and beach there is a home enlarged to accommodate the owner's visitors for food. Orders are taken on board the boat out to the island from Pythagorio. They serve BBQ'ed lamb or pork chops with standard Greek condiments and drinks. Lodging is not anymore possible, unfortunately.
The boat departs Pythagorion harbour about 9am and picks up people a couple of more places (Hereon), and leaves from the island about 5pm. About 1 hrs ride.
The little village and now tourist place Kokkari on the northern coast of Samos is such a nice place. Go there because it is nice and colorful!
When you plan your trip to Samos, check if the wind conditions at the time of the year are favourable - if not, you may have to cope with strong winds. They tend to die down by late afternoon, though. If it's very windy, find somewhere else to stay overnight, but be sure to come here and visit.
There are plenty of hotels, pensions and restaurants to choose among, and you may probably not have to book ahead.