What is this 6" vent coming out of the main furnace trunk going under my deck for?
It's an outside air (intake, probably, but you don't specify direction of airflow.) 

Can be a simple system that forces some ventilation by bringing in fresh air all the time, can be a more complex system that alters the amount of outside air with a damper depending on the temperature inside, and outside, and called for by the thermostat (ie, so that you don't run the AC to cool off the house when you could just suck in cool air from outside the house.)