I love Arduino and my research mates and I use it often to prototype lab equipment. We are interested in a low-cost, permanent solution to replicate the microprocessing functionality of our Arduino once we finish prototyping. That is, we develop a first generation implementation with the Arduino. Then we would like to purchase a dozen ICs with our processing code embedded so that we can replicate our system. What vendors provide this service? What is it even called?
So you have a design based around arduino connected to some parts on an adjacent perfboard or similar and now you would like to turn that into a custom PCB and make a dozen copies?
A lot of us can do that for you. You can see designs I have done at Cross Roads Electronics
I can design the board so you can easily assemble it with thru hole components, or SMD if you have more soldering skill.
Bare boards are not expensive, and I can supply a PL for your to purchase.
Or I can build the boards for you.
You could do a lot worse than to have Crossroads do this for you! If the quantity is high, you can buy the CPUs programmed from Digikey. This adds a small cost to each CPU, but they come all programmed and you won't need a human to hook up a programmer and upload the app.