When I make a manipulative activity that I know I will want to reuse, I make each copy in the class set on a different color paper. I do this so that the pieces don't get mixed up: if I find a stray piece on the floor later on, I can return it to the correct set. I laminate the sheets, cut apart the pieces, and place each individual set in a small bag and stick the small baggies in a large freezer bag.
Some of the things that I've used this for are (1) dominoes (2) letters of the alphabet (for spelling practice), and (3) activities from the Teacher's Guide of El Nuevo Houdini.