This doesn't seem like a problem at all. In fact the AmigaOne boards already ship with LinuxPPC installed, and a version of the UAE emulator that runs under Linux. I believe that UAE was written for Unix first, MacUAE is actually a port of the Linux UAE. This is the link to the UAE homepage, which is Linux centric:
http://www.freiburg.linux.de/~uae/Hope that helps.
