Well, I looked at both and couldn't see were either supported the "CnQ" feature or S3 suspend. Those are 2 cool features I would look for.
The manual says the GEFORCE 6100-M7 doesn't support WN98SE or ME. So I guess you'll need to use 2000 or XP. Don't know if that is a issue for you or not. It does have a fan speed controller and Hardware Monitor. I couldn't find much on the MSI.
I would email both companies and ask about S3 suspend (if you want fast turn on's), CnQ (if you want to have the CPU run cooler and quiter) and fan control. I think those features are really good for a CarPC.
I would start reading the Newegg reviews and see if there are any issues you should be aware of. Make sure they have the feature you are looking for.