I would buy the Fodor's guide to Scotland when planning your trip. It has tons of information about what to see, where to stay, etc. I used it in planning our trip, and referred to it every day while we were there. We went in October, and apparently were really lucky with the weather. It was cold and overcast most of the time but didn't rain much while we were there. When I go next time I will probably go in September, mainly to beat the summer tourist rush.

I second Daz's list and would add Fort George and the Clava Cairns which are near Culloden. Also, Bannockburn is worth a look; it's near the Wallace Monument at Stirling.