I found a bunch of new leads last night. Seems there is a .NET Micro Framework targeted towards embedded devices.

http://www.netduino.com/

The project is to design our own 3rd party board running Windows CE. However for the proof of concept we are using various research boards and thats where I found GPIO pins and they are exactly what we need to have on our board to interface with. Adding other legacy ports like the parallel and serial ports wont suffice as we need two way and several pins of communications. The parallel port was close but other than shotgunning two parallel ports and cables to provide all the traffic its kludgy and costly.