I need a very simple connection between two NETMF boards. I dont want to setup CAN, Serial or other link between them so far, as its just a simple yes/no signal required.
I am guessing that I need a resistor or maybe even a diode in the circuit between them, what is the general recommendation there?
You would choose carefully to use a port that was in the mode you want. If you chose an output port as an input then you are not doing due diligence in your design.
Most ports on microcontrollers are in the default INPUT state so you would choose one of those.
In that case, your only issue is to prevent excess current draw from the switched off device. I would use a diode to avoid any current draw from an output port on your always on device with a pull-up or down resistor on the one that is off. The diode direction would be chosen depending on whether the output port is in the current sink or source state.
This is your only real concern with this and is easily taken care of with the above diode and resistor.