My suggestion would be for you to ground the case to the vehicle's frame. You can do so with a fuse inline or a resistor if you're worried the case may be "live", but chances are it's not.
My company is working on a 12V input, multiple output DC-DC converter that is fully ATX compatible at the moment, but it won't be available for commercial sale for a couple of months I'll keep you posted...
All you need for ATX is a +3.3V output in addition to +5V from your power supply. You could use one of the currently available supplies and add the +3.3V output to it, or build your own from scratch. Maxim ( http://www.maxim-ic.com ) and National Semiconductor ( http://www.maxsemi.com ) are excellent sources for switchmode DC-DC converter components.
You will also need to watch out for the +12V line -- I don't recommend feeding the car's 12V directly to the motherboard & peripherals like many people do, or using a linear regulator (i.e. LM7812) -- the car's 12V can fluctuate from 8-16VDC and is very noisy to a computer. Look into building a flyback converter to convert 8-16V into steady, regulated +12V.
You will need to be able to solder and follow schematics to build a supply though... they don't offer kits or any details other than schematics and electronics equations for figuring resistor values, etc.
DC-DC converters are great because they usually operate at several kHz and therefore don't introduce any audible noise into the audio path.