We have been thinking about making the proto boards stack able.
A proto board with an area for prototyping would be nice, but there is not much room for that. Would you want surface mount or through hole?

How about both? I am comfortable working with SMD, but it takes practice and your average Arduino user may not be. Having a through-hole version would appeal to many users (though you make the best use of the space with SMD)

(belatedly) vote for this as well, especially if a barometer/pressure sensor/altimeter is included. I was going to propose MPU-6050 as gyroscope/accelerometer with HMC5883L magnetometer and BMP085 pressure sensor.

All 3 on one TinyDuino shield would work great for my avionics project. I would use one processor board, one IMU board and one microSD board (or alternatively a I2C EEPROM on a proto board) to log flight data for my model rockets. The rockets themselves are small (2 ounces without engine) so every gram I save counts.