microcontroller for custom laptop
For anything to run linux, it can't be a simple 8 or 16 bit microocntroller. Your best bet is an ARM based system, in particular Cortex A8 or A9. Basically aside from the raspberry pi you've got beagle board, beagle bone, panda board and a few similar other boards.

I'm not sure there is a custom apps processor module available in general. If you're an OEM then of course you can find something.

If you are willing to build your own solution you can make it very small.