I don't have a lot of printed maps, but I store my flat artwork in one of those paper portfolios you can get at any art supply shop for $3-5. Also get a nice heavy piece of cardboard to sandwich the paper against the side of the portfolio so it doesn't sag. Or you can simply lay it down flat if you have somewhere to store it that way. Just don't put heavy stuff on top of it!
I used to have a cabinet with a lot of very short, but wide and long shelves that was perfect for storing art and paper, but I had to leave it behind when I moved—No room for it in the tiny apartment.