Seeedstudio offers this so called "Propaganda PCB service" , check it out at http://www.seeedstudio.com/forge/wikka.php?wakka=Propaganda.
You email them the Eagle board file (must be open source) and they send you 5 boards for $30.
I had the shield for the 8x8 RG LED matrix made by them.
Theoretically, you should be able to buy the boards I designed from their website, although I did not see them posted yet. Just ask. Anyway, I just finished revision 1.1 and I will get it manufactured in bigger batch.
As for the arduino, I used one made on the small prototype shield, since I wanted all the boards in the sandwich to have the same dimensions, and also because I wanted to eliminate some components (from the original arduino) that I did not need and which took some juice out of the batteries. I almost finished the design of this board (waiting to get a few more components). This should be also available soon.
After much thinking, I came to realize that Mr. BroHogan's original "sandwichduino" is the best approach for this kind of project. And coming up with a case is as challenging. The glass dome I used is not cheap, but the cherry case required even more effort, I assume.
The project is still in development, since I plan to add a few more things, as suggested in previous postings here.