I have several and store them much like I store my vinyl albums (for you kids, vinyl albums are giant CDs made of fossil fuels and covered with grooves.. )- stored upright with 'bookends' to keep just enough pressure on them so that they don't sag or stand diagonally.
Also, if the inner sleeve is the cheap-o plastic one, I used to replace it with an aftermarket plastic-lined paper sleeve. That may not be better storage exactly, but it was a heckuva lot easier to take the discs in and out.