Hacking the ArduCopter Software
For future Googlers, 

There are now (Jan 2014) much cheaper Flight Controller boards that use a ported version of ArduPilot (APM). Look up MegaPirateNG and you'll be pleasantly suprized.

So to answer your question, yes, you can port it to different boards, but the hardware out there now is so inexpensive (~50 USD), and the software so good (Mission Planner from ArduPilot and MegaPirateNG firmware) that it only makes sense to port it if you are


doing it for a personal or school learning project
have a very custom board that makes more sense to keep and use than going with an already debugged and tested Flight Controller.


Note that the size of the firmware is pushing the limits of the current AVR on these Flight Controllers, so a "small Arduino" will likely not be big enough.


Shameless self promotion: I wrote a paper on Flight Controllers for school a few weeks ago and am in the process of building a quadcopter based on MegaPirateNG's port of ArduCopter firmware. (If you want to see the build blog, there's a link in my profile.)