Chad is correct. There is no one method of cleaning water that works in all conditions. Waterborne pathogens are the easiest to remove. The last I heard, we still had no waterborne viruses in the US, so good filters, boiling, and chemical treatment all work. But heavy metals, organic and non-organic contaminants are another problem indeed. A good filter will remove some of these contaminants but not all. And they are everywhere. There is a mountain stream not far from here that has naturally occuring arsenic in it. Boiling does no good when this happens.
As Chad pointed out, know your water sources, prepare to deal with the problems they present. If clean water in your area will require distilling, then better get a still set up. My question is, how do you remove radioactive fallout from water? If I lived along some of those eastern rivers, I might have a lot of questions but out here, our water is reasonably safe with just filtering or boiling. However, if rumors about Fukushima prove to be correct, radiation may be a problem in the west very soon. But Fukushima or not, I would like to know how to deal with radiation other than deep ground water. Any ideas?