If you're taking a car I'd recommend the Pentland Ferries route from Gill's Bay.
My biggest disappointment was House 7, covered and inaccessible, at Skara Brae..........but the site is still very impressive for all that.
As someone else has said, when you're at Stenness, DON'T miss Barnhouse, tucked away behind.....it's a clue to the nature of what is being revealed at Ness of Brodgar just up the road. As for the Ring of Brodgar........stop off there when the crowds are elsewhere, if you can.
2 stunning places to walk are The Brough of Birsay and Hunda Island. The latter is accessible on foot by a causeway off Burray.