A smelly AC is almost always due to water collecting in the system. Be sure your drains are clean. The water promotes the growth of mold and mildew.
Replacing the cabin filter is a start, but will not likely eliminate the smell already there. For this, it's recommended that you use an anti-mildew spray, sprayed directly into the car's ductwork. There are several of these products available such as:
http://www.autogeek.net/1z-einszett-klima-cleaner-air-freshener.html or
http://www.allergystore.com/mold.htm. You can use Lysol, but this won't be as effective, will take longer (more applications to work) and you may not like the fragrance it leaves.
The way to prevent future mold and mildew is to switch off the compressor a few minutes before your destination and just run the fan, drawing in outside air to evaporate any moisture in the ductwork and the evaporator and to make sure your drain(s) are clean.
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