I never had any issues pop up from keeping games in their original cases, so that's where I keep my games when I'm not playing them.

If I buy a game second-hand though, it's sort of depends on the condition of the case it's stored in whether I keep it in that or store it in a CD case... No lie, I had to settle on purchasing a couple of games that came in an envelope type of thing (no case, no manual... sad times... ). There's no way I'm keeping my games in something like that, so into the CD case they went!