For Machu Picchu, you don't have to go with an organized tour, but I'd have to say it'll be more interesting. There are no signs, or anything, that will tell you what you're seeing. Getting to it from Cusco, via train, then with a bus transfer, and then a hike, would be a whole lot easier if you let someone else organize it for you. On the other hand, you might prefer just to wander and look, without the historic and cultural commentary - it's all a matter of individual preference. I'd also second, that if you're up for alot of walking, you take the 4-day Inca Trail walk, which does require that you go with a guide, and you'll see lots more than just Machu Picchu. The Sacred Valley, the historic sites around the city of Cusco like Sachsayhuaman, Pikilacta, Tipon, and others, are well worth the visit.