To reduce the confusion of having a stash containing both washed and unwashed fabric, I put a tiny safety pin in the fabric that has been washed. I do wash all of my fabric before using, but not necessarily right away. For small scraps, I have Ziplocs for each of the various colors or for finished projects. I put a small piece of paper in each bag saying "WASHED." If I happen to have a bunch of non-washed fabric, I do the same thing but with an "UNWASHED" notation in the bag.
I do the safety pin thing with batting remnants that have been pre-soaked.