Machu Picchu is the obvious highlight when visiting Peru but there are a number of fascinating sites in that area that most tourists miss.
The typical journey starts in Cusco, then by bus to Ollantaytambo, then train to Aguas Calientes, then hike to Machu Picchu.
On a Rick Steves podcast, his guest, a veteran South American traveller notes the sites around Cusco that are definitely not to be missed. Most notable is Choquequirao (pronounced "CHALK'-y-keer-RAO") which is bigger than Machu Picchu. Alpaca Tours have a 6 day walking tour of Machu Picchu to Choquequirao. A (slightly) easier method is to take the 4.5 hour bus ride from Cusco to the town of Cachora. This is most common starting point for the trek to Choquequirao, but it still takes 4 days. Andean Wings have a thorough description of the journey.
Look into other sites:
Tambomachay
Sacsayhuaman - 2 kilometers north of Cusco
Q'enqo
Ollantaytambo
Pisac
Rainbow Mountain (Vinicunca)
Humantay Lake



