Jameco.com has an interesting article on how to build your own Arduino microcontroller circuit.
The circuit relies on an ATMega328 microcontroller, and since it requires only component parts it is cheaper and has a potentially smaller footprint than the popular Arduino Boards.
We have started using Arduino microcontrollers to directly control the LEGO Motors (9842), and expect to post on this sometime in the near future. In the meantime check out posts on LEGO NXT motor control:
LEGO NXT Motor Wiring
Hacking the LEGO Mindstorms NXT Standard Motor