What are my options (ie purchasable hardware) for a COTS 32-bit Cubesat motherboard, that has successfully flown in LEO, running Linux? Do not suggest any hardware that has never flown in space before.
I know this is an old question, but since there isn't a single answer... A few years ago, Tyvak was offering its Intrepid System board. It is no longer in their product offering, but they seem to still offer boards, and still talk about Linux. Start with this page: http://www.tyvak.com/platform/microsat-solutions/
Other CubeSats have flown with Linux, but I haven't heard of those boards be made available for sale.