I believe that Giardia often gets blamed for diarrhea in backcountry travelers when simple oral-fecal contamination is probably the far more common cause. Good sanitary, hand washing, disinfection and field kitchen practices will prevent this.
On a related note, there is a commercial hand sanitizer called "Qore 24" that we've evaluated as vastly more effective than alcohol based hand sanitizers.
http://www.qore24.com/When backpacking, I generally use a four liter Platypus bag to collect untreated water. I typically let it hang overnight, bleed off a bit from the bottom to remove any collected sediments, and gravity feed the water through an inline filter into a 3L Camelback and a 1L Nalgene bottle. If I'm being extra careful, I'll add some iodine and let that work overnight as well.
Aquamira's inline filters that promise Viral as well as bacterial removal, in their "Red Line" series, looks interesting, and I'll probably buy one next.