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I did this myself a few months ago. When I did it they didn't have the nano-itx boards out, just the micro-itx. But it's still only 17x17cm.
I use mine for mp3s, dvd playback, gps navigation and OBD II diagnostics. Like you I didn't want to use a case, so I ended up placing the mobo in the center console between the two front seats. I got a 7" touchscreen LCD that I mounted above the rearview mirror, where I can glance at it without moving my head. I'm not sure how much you want to spend but you can get a 7" w/ touchscreen for under $250.
As ggadgit was saying, a dropout regulator is the way to go. Get one of the atx power supplies that VIA makes for their mobo's. They work off of 12v DC and can be put inline with the dropout regulator. In addition they're so small that they clip onto the motherboard itself with no wires. The regulator that I use actually starts and shuts down your computer for you whenever you turn your car on or off.
As far as your HD, I'm not sure that you'll be able to boot from a USB hard drive. I ended up putting a regular 3.5" under the front passenger seat with an anti-shock mounting system. Since you already have a laptop HD you can just get an anti-shock mount for a 2.5" drive and use it with an IDE cable converter.
I'm running a stripped down version of WinXP instead of Linux since all the functionality that I wanted wasn't available in Linux. Namely the OBD II interface program. For the Winamp interface I used the Comtrol program that lets you have over 15 buttons interfaced through the serial port.
I'm not at home right now, but when I get back I can post pics of how I did everything and links for where I got it.
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"Empirically observed covariation is a necessary but not sufficient condition for causality" - Edward Tufte
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