I recently wrote a firmware package for the ardupilot / APM 2.5 for use as a sensor and I/O board. This strips out most of its logic and pumps sensor data up the USB as fast as I could make it go while simultaneously reading USB commands for publishing to servo motors.
It also will mux between input servo commands and the USB commands based on an input channel’s value.
Post here:
http://www.diydrones.com/forum/topics/code-for-using-the-ardupilot-with-an-onboard-computer-usb
Code here (in the ArduRead folder):
https://github.com/andybarry/ardupilot/tree/arduread
04/17/13