i lived in peru for many years and backpacked around cuzco quite a few times. make yourself a favor and don't spend less than a week there. there are so many beautiful things to see. i don't know if you are a hiker but there's this place called Ausangate 100 mi. south of cusco. it's amazing.
and Choquequirao, almost outside of cusco. it's very similar to machupicchu, and the view is excellent. one of the most beautiful hikes i've ever done.
and try to make it to lake titicaca, as courtney said. if you plan to spend some time in bolivia go to Salar de Uyuni, the world's largest salt flat. it's wonderful. about 200 miles south from lake titicaca. and my favorite bolivian town, Samaipata.
i'll post more information and tips later when i get home. oh, and my friend's brother is a tour guide in cuzco. i can give you his information just in case.