I don't know or at least I'm not convinced about most stomach ailments being a water problem. I know we are all careful with filters, bleach, tablets, chlorine dioxide, boiling water, et al. but I think the majority of our "beaver fevers" have little to do with giardia and the like but rather good old e-coli and samonela. I think a good portion of our ailments are either a result of poor food handling and simply poor personal hygiene.
The Backpacker's Handbook by Chris Townsend has a pretty good section on water safety.
Townsend makes the point that in the North American backcountry, cleanliness and personal hygiene are more important than treating water for avoiding sickness. For example, he refers to a 1995 study published in the journal
Wilderness and Environmental Medicine that suggests that giardiasis and other gut disorders are spread "by oral-fecal or food-born transmission not contaminated drinking water." He said that of 34,348 reported cases of giardiasis reported to the authors that only 19 were associated with contaminated water and only 2 of those were known to be campers or backpackers.
He also raises a good point that hydration is more important than treatment when it comes to water. He suggests that avoiding dehydration is more important than ensuring all your water is treated (in the North American context at least, I assume).
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