Oracle, your post begs the question: how are prices of $5 for the PCB and $28 for the kit "so high compared to what the the parts and small PCB are worth"? I assume there's a markup to cover the time spent packaging kits and processing and shipping orders, and that doing the math would boil down to minimum wage or less for the dedicated RRRF folks...
Basically, I disagree-- the prices look reasonable to me. Saving money by making the board and sourcing your own parts will take time, so it's sort of a matter of what you think your time's worth.
While the Rep Rap goal is still a long way off, this stepper motor controller is a great example of an open source subsystem-- hoping this paves the way for more practical open source machines than 3D printers: home appliances.