Arduino had the advantage of being open source from the components up - you could make your own boards, and many did. Unfortunately, it seems that more recent models like the Yùn have broken that promise: http://www.wifi4things.com/arduino-yun-what-is-under-the-hoo...
The Atmel chip design is not a free hardware design, though. There actually are chips whose design is libre, such as the Parallax Propeller (under GPL.)
