My wife and I went to the Orkneys about 10 years ago. Hired a car and stayed at the Stepping Stones Hotel, bit pricey but comfy with a view from the breakfast room of Brodgar. Very short drive to the Stones of Stenness for the solstice sunrise and back for breakfast. Magic!
Plenty of car ferries between the islands but book a few days in advance. We took the car up to Westray by ferry and drove down to Ronnaldsay for The Tomb of the Eagles. Sounds as if it might have become a bit commercialised, pity but still worth seeing.
Apart from the major visits, Skara Brae, Maes Howe etc, don't miss the Italian Chapel. Not strictly within the remit of this forum but absolutely wonderful with its own story. I'll leave it to you to discover it for yourself.
Also, if you're interested in Orkney traditions and myths try Peatfire Tales
http://www.orkneyattractions.com/peatfire-index.html Nothing else quite like it.
All in all, one of our most memorable holidays.