I would take boiling as a last resort, low altitude, plenty of fuel AND time, long term solution... in any other situation, purifying tablets (Micropur Forte) + filtering shoud do the trick. I would like to try one of those stery-pen gadgets that generate UV radiation... seems like they kill pretty much anything alive in the water quite quickly.
I don't own (yet) a filter since I usually wander above the tree line and water sources are quite clean. Many times I rely on stablished fountains or seeps that (as stated before) are naturaly filtered. Melting snow is also a quite clean water source (sometimes it gets dirt or debris on it, but that will not kill you).
Boiling is something to do while in camp at night I guess... not on the go. If you also pack light, chances are you will not carry a big pot, so filling water bottles at 1l per batch... is going to take a long time.
Mikel