I fold them repeatedly in half, adjusting the last folds a little if needed so they all are the same size, with the last fold being a little wider than the other direction.
Then I store them (with the last fold up) in a standard size shoe box. It is easy to see what I have, and keep them all together in a compact space. The shoe boxes also stack well, as the folded FQ's are just about as tall as the box is deep.