I have a case from a 4x4" Kenko Technical Filter Holder that is just perfect for my 4x4" filters. I suspect you could find one of these old filter holders on eBay for cheap and buy it for the case.
For my 3x3" gels, lately I've been using a thing made by Moleskine, a company that makes nice little bound notebooks. It looks like a notebook, but instead of pages it has six file pockets, which is just enough to separate the filters into categories, and in each pocket I keep the filters separated by paper separators.