Please don't laugh, but I use the BIG cat litter jugs with the handles (my cat uses crystal litter). They can stack, they're "grabbable" and they live on two shelves on the wall so they're out of the way.
I sort by color mostly, with a separate jug for batiks, Christmas and Halloween. I also have a separate jug for leftover binding (that's been pressed in half and is ready to use on smaller projects) and bias binding tubes (each in its own ziplock to prevent tangling.
I don't use anything smaller than a 3" square, giving the rest to my guild's miniature quilt bee.