I use Outdoor Research heavy-duty waterproof stuff sacks. One for the sleeping gear, one for clothes, one for food. Everything else gets put in the little pouches on my custom ALICE pack setup.
Yeah they weigh more than their "ultralight" silnylon stuff, but I tend to be hard on gear, and the last thing I need is to tear the stuff sack that is carrying my sleeping gear, and then cross a river. Bad news right there...
Speaking of river crossings, those stuff sacks also hold air and can act as "balloons", so your pack will float if the water gets real deep.