Just like any other vehicle with A/C, your evaporator coil lives in a dark and wet environment. Perfect place for the developement of smelly bacteria. I've heard that using outside air (don't use the recirculate setting) for the last few minutes of your drive might help the A/C odor. Makes sense because oxygen is one of the best natural cleaners. If you take the vehicle to the dealer, they can hit the coil with a cleaner, but that's a temporary fix. While at the dealer, have them check the drain on the evaporator housing to make sure it's not blocked. If you smoke while you drive, keep the driver's window open a tad and don't use the recirculation setting.
As far as smoke smells devaluing a vehicle, I think it would to some degree. However, a good cleaning would take care of that as would placing an ozone generator (ie; sold at Sharper Image) in it overnight. A bowl of ammonia is supposed to draw out odors. I've even heard about placing clothes dryer softener sheets under the seats, if you like that sort of smell.