An Arduino isn't expensive, but that still doesn't mean that it suits your needs right out of the box. If you want to construct your own custom board, Make shows you how in a three-part series.
The Make build here uses the Really Bare Bones Board schematic as influence to make a low-power, tiny Arduino-style board. It guides you through building the schematic in EAGLE, laying out the board, and then finally putting it all together. It's a complex process, but if you've ever wanted to make your own board, or you just want a better understanding of how an Arduino actually works, this is a good place to start.