First, I decided on a physical form factor. If I was going to connect multiple modules together, it would be nice if they were all of a "standard" size. I picked a 2" by 3" PCB dimension for the AVR baseboard and for a large module. I picked two other sizes for smaller modules, 2"x1.5" and 1"x1.5". (see the first attached graphic "Module Sizes.png")
This effectively gives me a full size, half size, and quarter sized modules. It also breaks the AVR baseboard into what I like to call "quadrants". I've labeled the quadrants A, B, C and D. Each of the modules that I've built are built specifically for one or more quadrants. You'll see why when I go into detail on the ISP and Serial modules.
I guess there's not much more left to say, so let's move on to the board to board connectors.