As reported by South American Explorers:
The Instituto Nacional de Cultura (INC) has instituted new rules for the Salkantay trek. Now it is only possible to do this trek with an agency and additionally, they have implemented a new change of 120 soles ($36), therefore expect the price of the trek to increase accordingly. There have been other price changes. For entrance to Machu Picchu, the price is now 118.50 soles ($36).
… It is expected that in the next year, there will be similar changes to other alternative inca trails. For up to date information, please contact the Cusco Clubhouse, email@example.com.
What a drag.
Our advice is to avoid the Machu Picchu treks and hike out of far-less-regulated Huaraz, Peru instead.
UPDATE: Jesse posted a 2006 trip report.