You're thinking of bresoftware.com, who used to run another related site just for manuals and cases: videogameinstructionbooklets.com. They consolidated the case/manual site with their main site a few years back as stock started to dwindle. It looks like they completely stopped carrying anything but games at some point.
A lot of people said they got their items directly from the manufacturers, which I never believed, b/c everything I got from them never looked fully new.. these would be minor scuffing on the cases, indents on the cases/manuals from the cases, minor opening creases on GBA boxes, etc. I feel like they actually got their stuff from game rental places... and as those went belly up, so did their sources. No way to know for sure though.