I had always been vaguely aware of products intended to get rid of air conditioner odor, and I had read about some kits that allow you to install a fitting on the side of the evaporator housing so you can inject a foam-disinfectant directly. I asked at a local parts store about such a kit, and instead was shown a small spray can of stuff designed to be sprayed into the heater air intake -- at the base of the windshield -- seemed like it was worth a try, and was only $7, so what the hell, I gave it a try.
Short story: It works well. If you have odors coming from your air conditioner, get over to your local Car Quest and ask for the little can of stuff (I'm sorry, I don't have the name or part number with me now) and give it a whirl.
Three things: (1) Remove the cabin air filter first, and spray directly down into the blower. If you don't, all of the spray will simply end up in your filter -- you'll get the scent, but the disinfectants will never get to the evaporator and kill off the mildew. (2) The can recommends spraying for 10-12 seconds. I naturally assumed that spraying for 20 seconds would be twice as good -- maybe it is, but if you do, the scent is overpowering, like 55 gallons of cheap after-shave dumped into the car. Go with 10-12 seconds first, and if it doesn't work well enough, do it again in a week, after the scent has abated somewhat. (3) I'll bet your cabin air filter needs replacement, too -- mine was filthy, covered with dirt, leaves, seeds and all manner of crap, and had been nibbled by mice. $34 for the Bosch replacement filter at Auto Zone, $28 at NAPA. Steep, but filled with activated carbon, and it's worth it!