Planning to travel to Greece, including Santorini, Mykonos and Samos (as suggested by RS!) in Sept 2014. Will you please share your experience on B&B's, accomodations in those islands. In Mykonos family members stayed at Lino Apartments with excellent service (near Agia Anna). Ideas please?
If you are adventurous, you could get a room on arrival at any of the islands from the many people meeting the boats, done that several times with always pleasant results, as long as you know about where on the island you want to stay. For Mykonos, look in Lonely Planet or Lets Go Greece for decent budget recommendations, just watch out on places near the Mykonos Town center, even in September the clubs go all night, adding to the noise.
For Santorini, search this board, an often discussed topic, you'll find lots of options.
Samos is a long way off the central Cyclades route of Mykonos and Santorini, getting there by ferry will mean a long ferry ride, maybe overnight or having to stay somewhere else a night since there is likely not a direct ferry between either of the other islands. You may look into flying or maybe reconsider and find an island closer to your route. If so, I would recommend a quieter Island...Folegandros, Paros, even Naxos, maybe Milos.
September is a wonderful time of year for Greece. But I agree with Paul ... Samos is a looong ferry ride from Mykonos and Santorini. Even though it sounds appealing, it would be better to save Samos for another trip (maybe combine it with Ikaria and Patmos and a day-trip to Ephesus in Turkey).
Paros and/or Naxos are better alternatives for a trip that includes Mykonos and Santorini. Depending on how much time you have, you could even include Milos. For most islands, I find 4 nights to be about the right length of stay.
To find your accommodations, I like to look at reviews on Trip Advisor and Booking.com. On Booking.com, reviews can only be made by people who actually stayed at the hotel/b&b, so they may be more trustworthy. I also like Booking.com for making reservations. In most cases, you can reserve without a deposit and can cancel as little as 3 days in advance of your booking, with no penalty. Read each property's terms to make sure. I will often try to book direct with a property; often little island properties will also book with no deposit and a decent cancellation policy. However, if they DO require a deposit, I use Booking.com or look elsewhere.
Do a search of this board for sleeping recommendations. I know Lee has posted many recommendations for Santorini, and Janet has posted some for several other islands. I'm not familiar with Lino Apartments but it seems Agia Anna is a little ways from the main town on Mykonos; if your family members liked it, though, that may be just fine.
Finally, I would highly recommend that you plan your trip so that you fly into Athens and fly directly to Santorini on the same day. Try to find a flight (Aegean airlines) that leaves Athens at least two hours after you arrive in Athens. It makes for a long travel day, but it's wonderful to wake up on that first morning already on the island. Also highly recommend that you ask your hotel to arrange your transfer from Santorini airport to the hotel. Nothing better when you get off a plane than to see someone holding a sign with your name on it! After Santorini, you can ferry to your other islands and back to Athens. Be sure to be back in Athens at least two nights before your trip home, in case of ferry delays (uncommon but possible).
Have a great trip and come back if you have more questions!