I'd say 5-6 days is plenty to see the really good stuff, certainly on mainland. At least if y're able to spend most of yer time megalithing. Oh, and have a car (or bikes & energy!!!)

Firstly, I'd REALLY encourage you to get across to Rousay - the chambered tombs along the S coast are FANTASTIC & (mostly) really easy to get to!!!! (We didn't get across to any of the other islands that need a ferry for £ reasons, but wee hugely glad we did that one...!)

Hit all the usual suspects - Maes Howe, Skara Brae, Brogar, Stenness, Watch Stone, Unstan, Wideford Tomb, Fairy Knowe/Cuween. Don't miss the Tomb of the Eagles, Grain Souterrain & Rennibister Souterrain. Mine Howe's worth seeing but I was slightly underwhelmed.

Leafea is a nice place on a sunny day - esp if you walk there along the coast path. Long Cairn/Head of Work is quite a nice tomb (you can't get in - which is almost unusual in the Orkneys) - it's in an amazing position on a peninsula - but it can be a wild walk out to it! Wheebin's an ace monolith. Stanerandy's ok if you have time, as is Staney Hill.

Jane posted a cuppla blogs that might be helpful:

Rousay http://www.themodernantiquarian.com/user/1761/weblog/40

Deepdale stone(s) give(s) you a great overview of the Stenness, Brogar lot http://www.themodernantiquarian.com/post/30016/weblog/

love

Moth

If starting from Kirkwall you may want to get an Historic Scotland ticket from the Earl's Palace or the museum (the latter free, unlike Stromness, which has little to interst us anyway. Though the Grain earthhouse is free you can only go there during the week and need to get the key from Ortak jewellery first. If there has been any bad weather within a week or so the final drop to the Wideford Hill tomb is gey slippy, and even if you have got to the trail top by transport it is a bit of an awkward walk to get to the cairn. Rennibister earthhouse you might also want to avoid in bad weather, though at least it has natural lighting. Cuween Hill is steep but no too bad going up. Maes Howe costs to get in, they only allow small parties at set times (which means you might not be lucky), and you aren't allowed to take photos inside. Next up are the two circles and the Barnhouse settlement, all free. Skara Brae is a whopping £6.50 to get in, so not nice if you're strapped for cash late on. A visitors centre with a good restaurant and bookshop. Lovely long beach nearby. Brough of Birsay is tidal, which means you need to check if you can get there during your stay, and if so which particular day. At least it is not as dear. Broch of Gurness is also inexpensive and is a lovely undulating site to walk about.
If you go to the Italian Chapel with its fantastic trompe l'oeil artwork, this is free. If you can find the Sorquoy standing stone its a neckbreaker. The Howe of Hoxa is a nice little broch, though Petrie mucked it about a little. Down at the end of the South Isles of course is the Tomb of the Eagles, you have to pay the owners but they have a magnificent display and en route to the tomb a few yards detour to the burnt mound settlement is a must.
Mine Howe can be rather underwhelming timewise. A small fee to go inside, outside only the mound and exposed ditch wall. On the isthmus between St.Andrews and Deerness there is a brilliant beach through the sand dunes. Over in Deerness if you are interested in a Norse chapel take the road opposite Deerness Stores and have a look at Newark.

It must be 10 years since we visited Orkney, we caught the ferry from Gills near John O' Groats, to St . Margaret's Hope and vici verci. It's much quicker and cheaper than crossing via Scrabster