I did mine without a case and it's great. My JAMMA cab has a shelf that slides out, so I have the PC mounted to that shelf. I can slide the whole thing out and replace it with a JAMMA board or Dreamcast board easily. Here are some pics:
(http://www.pyronious.com/images/emulation/motherboard.jpg)
The motherboard and JPAC mounted securely in place.
(http://www.pyronious.com/images/emulation/motherboard1.jpg)
Installed inside of cabinet
(http://www.pyronious.com/images/emulation/motherboard2.jpg)
One more inside the cabinet
Good luck!