Until recently, the only real contender for a combination of Motherboard and processor with a low power consumption, and also importantly, low heat generation, was Via's range of Mini-ITX motherboards. These boards are designed to use a minimum amount of power, whilst still being able to run the same software as their desktop counterparts. The downside is that the processors are not particularly powerful or fast.
However, so long as you can survive without being able to run applications requiring cutting edge graphics processing, these are ideal for use as carputer motherboards. These mini motherboards are sold with the processor soldered in place, so there is no upgrade route.
If you are really tight for space and need to use the smallest possible size of main board, you can consider Via's Pico-ITX boards.
Further information about Motherboard Form Factors.
In spring 2008, Intel released a new processor called the "Atom". This had an
architecture which had been designed with a very low power usage. It was designed
for mobile applications of all types, including hand held devices. One of the
intended uses was low power consumption PC's.
The processor only consumes about 4 watts, however the chipsets
in the Atom Motherboards which Intel released, have an older design and are not
so frugal in terms of power requirements.
Even so, combined power drawn by the processor and motherboard combination under "no load" conditions, is comparable with the Via motherboards. Unlike the Via boards, putting the board under load makes very little difference to power consumption.
The introduction of a dual core version later in 2008 improved performance and made this a very attractive proposition as a low cost carputer motherboard. This an increasingly popular platform for carputers and is the one I personally use.