I ended up ordering a Via TC motherboard as it will take up less space
than the CL with cumbersome DC converter and hopefully reduce RFI, and
if there is still RFI I have only one variable to contend with vs two.

I did not go with the PC104 format although I did look at this at
length. I already have considerable experience with the VIA now, a case
and airplane bay designed for it (17cm x 17cm) and a very lean kernel
tweaked for it. Also the VIA is a tad more mainstream with this
typically resulting in better doc and support for drivers. Also I can
boot off a write protected USB flash card (USB flash memory as IDE did
not work for me, too much data corruption in unexpected power off
scenarios). I don't know which PC104 have this ability. Anyone with
PC104 experience would probably argue with this, but I have had my fair
share in the past of getting odd behavior with a video, sound, ethernet
driver and having to slowly track it down. I know all the MB sensors on
the VIA are queryable in linux (ie CPU temp, all the voltages, etc..)

For me, memory is very important and 512Mb a mininum. Why so big when
my entire custom Linux distribution with X and Java fits on a 128Mb USB
flash card? As a Robert pointed out the kernel is a small memory
consumer, X is the real hog. And with potentialy complicated displays
this would grow even further.

Most importantly this distribution runs in entirely in memory,
there are no writes by the OS to the main USB flash card which is write
protected. As such there is no swap space, and hence any malloc calls
need to actually find real memory not virtual memory. Flash memory
degrades with each write, areas such as swap and log directories can
receive an enormous # of writes with often little effort. Some
benchmarks have shown corruption after only 10,000 writes. Having a
memory block go bad (which is just a matter of time given the nature of
Flash) can lead to odd/unpredictable behavior (the worse kind),
something I want to entirely avoid.

The secondary USB flash card, which is not write protected, holds the
log files and mp3 files. 'Non critical' files. I also wrote the data
logging program to only flush the OS writes every X seconds, not on
each log write. I could add an OS swap file to this partition but I
still could end up with corrupted swap space and the additional writes
would also shorten the life of the USB flash card. Additional memory is
cheap insurance (in additional $40) in avoiding these problems and has
an added benefit of performance.

If I was going to start from scratch I might go with the PC104 platform
but neither platform seems to be vastly superior to the other. And the
Devil you know...