My safe water procedure:
1.) Mechanical Filtration: Varies in effectiveness depending on the filter diameter. This should never be your only method of making water safe, and really only helps the aesthetics of the situation, and the water only looks cleaner. This can be accomplished using any funneling system, but it is useful to have a tube of some sort that you can pack with filter material (coffee filters, cloth, charcoal bits or bits of burned wood, moss, leaves, etc., depending on your level of access).
2.) Disinfection: A couple drops of bleach should do the trick. Bleach kills organisms and destroys viruses. The chlorine is also "used" in the process, so there is a built-in rough metric for determining if there has been enough bleach added. Add a few drops, wait 30 minutes, smell. If you can't smell any bleach, add a few more drops. Repeat until you can detect any small amount of bleachy smell after 30 minute wait periods.
Mechanical filtration with professional water filters usually only filter organisms, unless they specifically say they filter viruses as well (viruses are MUCH smaller than organisms). Boiling can also leave viruses intact, but tends to kill all but the most crafty organisms (as Uthgaard pointed out). As far as drinking water without any kind of treatment, try to get as close to the source spring as possible. No spring source is 100% guaranteed safe to drink, but as you get above waterfalls and other natural barriers to wildlife, there is less chance for levels of contamination likely to cause illness.
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