I would recommend the 4 day hike on the Inca Trail. These days you are require to be part of a group tour. Q'ente and Andean Life are two that I remember off the top of my head. There are a few others. Of course, if you aren't much of a hiker, you should just take the train. You take the early train there and the late train back for a full day at Machu Pichu, or stay at the luxury hotel overnight and be at Machu Pichu for the sunrise when no one else is around (except the hikers who hiked in that morning and the other hotel guests).

I also visited Arequipa and the Colca Canyon (so-so experience, only saw around 3 condors that morning). The Nazca lines are very interesting, took a small charter flight from Ica (very turbulent and dizzying because the plane rolls side to side to allow people on both sides of the plane to view the diagrams out their window). Next to Ica is Huacachina oasis, also a "been there done that" experience but not much to do or see there.

That reminds me, how do I record that Ica to Nazca lines flight on flightmemory? We did a fly over and returned to Ica, didn't actually land there...