I find this discussion fascinating first, because there is so much conflicting information out there and secondly, because I used to work in a sterile tissue culture laboratory (on a mushroom farm) so I have some hands-on experience in what's involved in creating sterile conditions to grow mushroom mycelium rather than another undesirable organism. I don't think anyone will ever find a hard and fast rule about how long to boil for reasons already mentioned. But one thing to remember is that, unlike a food substrate such as a bag of rye grain which is easily contaminated by undesirable organisms, you are not defenseless. In other words, you will usually be ok drinking something other than completely and totally pure H20. Most infections by opportunistic organisms require a certain loading threshold - and your immune system is always fighting to make sure that threshold isn't reached. But if you drink water loaded with giardia and overload your immune system's defenses - well, you'll be having that unique experience of having stuff come out of both ends simultaneously. :barf:
Usually, bringing water to a boil is sufficient - if it makes you feel better, let it boil for a few minutes. However, what isn't necessary is multiple purifications - treating with chemicals and/or mechanical filtering and then also boiling. If you didn't have an immune system or if it were severely compromised, then yes, you should only drink totally pure, distilled water - and you should also live in a bubble.
This is basically the reason why people in developing countries drink some pretty bad water and they're ok - but if you visit them and drink their water, you're going to get mighty sick. Their immune system is tough and prepared for the loads applied to it - and yours isn't. So besides boiling water, keep your immune system in shape. Eat vegetables, exercise, get regular sleep - and don't stress about nasties in that sparkling mountain stream. Just bring it to a boil and you'll be fine.
EDIT: Just thought of something - this is a good reason to carry electrolytes in your PSK or FAK. If you do get severe diarrhea, you'll be better able to survive it if you can easily replenish your electrolytes.