Modern Device’s Really Bare Bones Board is an Arduino clone designed to have an incredibly small footprint. It’s barely wider than the requisite AVR and is laid out so you can reduce the size even further. Don’t need the power connector? Just snip it off. Don’t need the voltage regulator? That can be removed just as easily. The kit is only $12 and all through-hole components. [youevolve] posted a build guide that shows exactly how easy it is to assemble.
Related: Freeduino SB 2.1 review