The air conditioner system has been a little stinky as of late. Most likely due to moisture/mold building up. In the future a good way to resolve this is to run the economy air for a few minutes after turning off the AC to flush out the moisture. Also replacing the cabin filter regularly will also help.
After doing some research on mold and smelly ac systems, I decided to purchase Klima-Cleaner to clean the air conditioning duct work in my car.
Its very straight forward to use, just attach the supplied tube to the bottle and stick it as far down your center vent as you can and empty the whole can in there. Let it sit for a bit and then run the air conditioner for a minute or two. The directions will be right on the can.
Between this cleaner and replacing the pollen\cabin filter it resolved my stinky air conditioner issue in one single treatment.