Depends on what you're looking for.

Orkney is the most obvious place if you're interested in meso and neolithic sites, such as Skara Brae, Maes Howe, Stenness and Brogar. For brochs, visit Glen Elg - or Shetland if you can be bothered going all that way. Caithness and Sutherland are spoilt for tombs and standing stones. The Isle of Lewis has probably the best stone circle in the UK, at Callanish, and that area is dotted with many circles and single stones. The well preserved Carloway Broch is nearby too. Pictish stuff is all over the north, but Moray and Aberdeenshire have the greatest concentrations of them. Roman stuff, there's not much, but the Gask Frontier between Perth and Stirling represents the first time the Romans stopped advancing in Britain and established a northern limit on their Empire. There are a few forts, but they are just earthworks. The Inverness/Dingwall area has vitrified forts at Craig Phadraig and Knockfarrel that are worth a look, as well as the Clava Cairns, Culloden battlefield, etc... Whatever you're interested in, archaelogically, there's somewhere in the Scottish highlands for you. Further south, Lothian has a few good standing stones and ancient forts.

You'll have to make a number of strategic choices one being do you go for
1) the "big name" sites on the islands (Orkney, Lewis) accepting that narrow roads and ferry timetables will considerably limit how much you can get round - but you will come back having seen the best of Scotland, or
2) stay on the mainland (probably south of the Great Glen where the roads are best) and get round many and a more varied selection of sites.

Here are some thoughts on option 2 assuming you have 14 days. Where I've mentioned sites by name, they are usually Historic Scotland or Local Authority run so you'll get info boards, parking and easy access. They'll be a bit manicured, of course. Worse still, there may be other people there. But if you don't know Scotland, it might be a good place to start. They won't fill out the day so you'll need to add some others from what's on TMA.

Obviously, you could do this in reverse depending on your most obvious entry point to Scotland - Berwick or Carlisle.

DAY 1
Get to Scotland. East coast Borders. Edinshall broch (not a typcal one).
DAY 2
Around Edinburgh. National Museum. Cairnpapple henge (check opening times). Glenrothes henge, mortuary enclosure (?), stone circle with rock art.
DAY 3
Angus souterrains and Pictish stones/Museums.
DAYS 4/5/6
Aberdeenshire stone circles and Pictish stones.
DAY 7
Clava Cairns and Corrimony.
DAYS 8/9/10
Kilmartin Valley. A bit of a drive from Corrimony but not really worth bothering with anything in between when you'll see better at Kilmartin. Rock art, stone circle and alignments, henge, chambered cairns. Great wee museum. A mainland must see.
DAYS 11/12/13
Another longish drive but worth getting down to Dumfries and Galloway. Cairnholy chambered cairns, Torhouskie stone circle, rock art. Ballochmyle worth stopping at on the way.

Hope that helps.

It depends how far north you are intending to go really.

If you are planning as far as Glasgow and north of that then I would recommend the following:

Fistly I would urge you to try and see Ballochmyle.

http://www.themodernantiquarian.com/site/156

It is a bit of a detour if you are heading generally north but I guarantee its a jaw dropper. The pictures dont do it justice cos its _big_ it covers two large sandstone walls. My somewhat doom laden post about it doesnt really mention the fact that we were totally gobsmacked when we came through the wood and got a first look at it! Simply stunning.

Next head for Callander and onto Loch Tay

http://www.themodernantiquarian.com/site/175

and surrounding area. There are some great spots to camp next to the Loch (on the opposite side to Killin). Now is a good time to visit Scotland cos the midges dont get really bad until the summer.

http://www.themodernantiquarian.com/post/16647

Back up the road to Crianlarich and onwards to Kilmartin (you might have to go back down the road a bit to the Tarbert turn off on Loch Lomond). There is probably a quicker way but I have no map handy.

There is a good spot to camp just past Kintraw. Take the first left after Kintraw and keep driving past the marina until you come to a gate onto the tip of the penisula. There is a car park and a small piece of land to pitch the tent with views to Jura and the Corrievrechan whirlpool (way way way in the distance).

WM

If I could only see one site in Scotland (or possibly in the world) it would be Callanish. It's worth the journey.

Kilmartin! Kilmartin! Kilmartin!

Just DON'T go in the midge season

Thanks for the input people. There's some great advice in this thread and I'm sure I'll be able to put it to good use!