What standard connections are you using presently, and what power levels are involved,
As you gave an example of an ITX motherboard, does it need stuff like sata for storage routed out, or simplified to a network or usb boot
Is it 100mb , 1Gb, 10gb, etc networking you need, is it via ethernet, or other means, (to get an idea of impedances and frequencies)
What video connection(s) are you planning to use, VGA is more forgiving than HDMI for instance,
And how much power do you need to carry, you may need a twin plug back plane, one for high current power and one for I/O to keep costs down,