Arduino PC LED strip controller
I can see why you'd wand this since it'd be really nice to be able to reprogram the arduino at every time although having separate grounds while still connected to the same PC is going to get a little hairy.

The USB and the Molex connector share a ground internal to the computer so if you wanted to separate that, you'd have to modify the USB board to use a different ground.  This gets into heavy PC modding and can get pretty hairy quickly.