I have never had any problems with any water from remote areas that I know of, but I've always used chemical treatment, filter, purifier/filter, SteriPen, or some combination. I boil treated water for food prep purposes instead of water treatment.
SteriPen FAQ
http://www.steripen.com/faq.htmlFilters I own, use, and recommend:
MSR WaterWorks EX, MiniWorks EX, and HyperFlow
Katadyn Pocket and Expedition
Katadyn Base Camp and MSR AutoFlow
Katadyn Exstream Virustat bottles/kits
I own and have used others which have either been discontinued or I just don’t use any more.
If prepping water for use at night, I like to use a lightweight “bucket” to let the particulates settle before filtering. I add the chemicals while it is settling.
Before storing or when backflushing on extended trips, I like to treat the “clean” water with chlorine before the backflush.
Coffee filters are excellent prefilters.
You might think I spend excessive time, money, weight, and physical energy to make sure the water I drink is safe, but there are too many unknowns to risk it IMO. Anyway, the time to do this is relatively minor in comparison to some other backcountry activities.