With some older systems built before cabin air filters were standard, you might experience a foul odor coming from the HVAC vents. This is often due to mold and bacteria growing on the evaporator assembly. Think about it: The evaporator is in a cool, dark place and is often covered with moisture. It's a good place for bacteria and stuff to grow: stuff that can cause odors.
The best fix for this is to remove the evaporator and clean it with soapy water. This is an expensive and time-consuming process, to be sure, but it is the best way I've found to deal with the problem. However, there are products that can sometimes solve this problem without requiring the removal of the evaporator. These products are sprayed into the air ducts and ideally work their way down to the evaporator, where they can clean off the offending mold and bacteria. This is often a pretty good fix and is easily repeatable.
One way to help prevent the bacteria from taking hold in the first place is to run the blower motor with the AC off for the last five minutes or so of your drive. This will help dry the condensation on the outside of the evaporator and prevent bacteria from growing there in the first place. If you run the heat for a little bit, it's even more effective, although a bit uncomfortable in the summer.