Nearly all of my disc based games are in their original cases, so this is a moot point. I store the cases in boxes or tupperware containers, which are separated by system.
If I don't have the original case, I'll use the following methods:
-regular cd jewel case for Sega CD, 3DO, Saturn, PS1 and Dreamcast games
-cd slimcase, only if I don't have a regular case
-regular dvd case for PS2 and GameCube games, if I don't have those then I will use a cd case until I find a good dvd case for those type of games
Last Resort: plastic cd case (like you see used with some computer discs, found at Staples) or a paper sleeve (also used with some computer discs).