I am totally sold on the Aloksak zip lock interior bags that come with the AMK Ultralight kits. You can also buy them separately: REI Aloksak 4 Pack

They're clear, 6 mil, and waterproof to 200 feet. They also seem more flexible to me than most Ziplocks, which helps resist punctures.

I also get a lot of mileage out of the 4 mil Elkay poly zip top bags for things that don't want to get wet while I'm hiking -- cell phone, driver's license, etc. They hold up a lot better than your average freezer Ziploc. The freezer Ziplocs are more compact, so I always throw a couple in my gear (both quart and gallon size), even if I don't know what I'll be using them for, whether I'm hiking or traveling. Invariably, when I get back to civilization I've found a use for every last one of them.