After eliminating the Netduino, I've chosen the Arduino platform for my prototyping. Here is the form factor for the Arduino Uno board. As you can see, for the most part the connectors expose the micro controller's i/o pins.
Prototyping can be accomplished by either a bread board of jumpered components, or with some inexpensive plugin modules similar in concept to Gadgeteer or GoBus, or probably a combination of both.
I originally started down the path of breadboards and components but discovered a module based component system from SeeedStudio called Grove that will help me prototype. The plugin components are called twigs, and they plug into a SeeedStudio Grove base board shown here:
So my first order was a SeeedStudio version of the Arduino Duemilanove called Seeeduino V3.0 (Atmega 328P). As of this date it is in transit.