Trying to organize tupperware lids is like trying to fit a square peg in a round whole... literally. You can't keep the lids with their plastic container because it takes up too much space. You can't put the lids in one drawer and the base in another because it takes forever to dig and find the right match.
Finally I've found the answer - just put your lids inside the biggest tupperware dish. Look how neat and tidy it makes my little shelf. Problem solved!