Also, you might be interested in this Arduino bare-bones kit. It has an ATMega chip with Arduino bootloader installed, as well as enough parts to make a home-brew arduino board. It is the UNO version of the Arduino, but allows you to custom make an arduino application without having to mess with the Arduino circuit board:
I have used these in the past, and all you need is a USB/serial board that you can get at SparkFun to connect the system to the Ardunio programmer.
BB-ARDUINO: JAMECO KITPRO: Education & Hobby Kits
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