I, too, use plastic bags, but have some (we won't say how many!) in the heavy plastic zippered covers you get when you buy pillowcases, sheet sets, or other bed linens. They are very sturdy and hold up well. As others have said, labels, instructions, and notes are very helpful, as well as putting in any specialty rulers or templates. Sometimes my notes include web addresses where I can find instructions or tutorials for a particular technique or block.
Hope you find a system that works well for you. It can make all the difference between ease of effort and frustration.