Anything that I don't want to get wet and that I won't need while hiking (so stuff like my quilt, pad, any insulation for in camp, etc.) goes into a Litetrail.com packliner (nylofume bag) that gets closed up and put in the bottom of the pack.
Everything else goes in on top either loose or in its own small cuben stuff sack. Things like my shelter or my cookpot/stove are put in small cuben stuff sacks. Wind jacket, water filter and other odds and ends just go in the top of the pack loose. I've got a small cuben stuff sack that contains all of my small items like my toiletries, repair kit and first aid kit.
Food is stored in a litetrail.com odor proof (nylofume) bag and then put inside a cuben dry bag from lawson (serves as bear bag in camp). If I think I might have some wet weather but want to have a midlayer or something handy and not packed away at the bottom of the pack in my packliner, I'll use the cuben food bag to instead keep those clothing items protected, but accessible at the top of my pack, while hiking.
I've never bothered to weigh what my nylofume packliner and food bag, and few cuben stuff sacks weigh but I can't imagine it would amount to much. Either way, I'm confident it's worth the miniscule weight penalty to help keep my stuff clean, dry and organized.