Create a circuit that can flash IR LEDs at 38.5kHz and be turned on or off by microprocessor
You can tweak the frequency with the 5k potmeter. I think you can get a pretty good range with that. If it's not enough, you could probably change the other resistor to something or a little larger value so the frequency drops.

To make it possible to switch the LEDs on and off I would probably a transistor (or a MOSFET) after the two leds. You could then connect the base or gate to your netduino with a 1k resistor or so. It doesn't start/stop the circuit, but it does start/stop the LEDs which I think is the result you want to go after.