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 liberal use of hand/face washing and even alcohol based cleansers would do much to reduce these problems. When you are camping by yourself, you are dealing with your own issues but in a group you may be dealing with others with less than ideal hygiene practices. All it takes is one person to forget to wash up after a bio break. Then everybody grabs into common snacks, meats and cheeses, common utensils, etc. and the potential for spread of bacteria increases. Now, put your food back in the pack and let warm temperatures incubate them.
I've only had one real intestinal problem from camping in my life -- I got the runs. And that was more likely due to not filtering "milky" glacial water more than anything else. Uncomfortable yes, but also a problem because I only had 1 set of underwear so other people on the trail "knew" I had a problem too!

I use an old Katadyn Hiker filter but prior to starting a trip, I check out the filter itself. If there is any question at all about the filter material, I toss it and replace. I have been know to boil and thoroughly dry the filter as well before the trip. Other things like keeping the tubing clean and the hydration bag sanitized, mouthpiece clean, etc. are also good practices.