I have had the same trouble with my old 94. My 2000 model has not had it but I'm sure it'll happen. The "stink" was mildew and mold that builds up inside the moist environment when the AC is on. There are products at any auto store which are aerosol vent cleaners. Spray it into the air intake (below wipers on the pass side) and it kills all the nasties. I have heard that some of the cheaper products can erode the evaporator core in some cars so get a quality product and follw the directions.
The prevention is to turn on the heat once and awhile to warm up the air ducts (I do it once a week for 2 mins at a time and blast to the floor).
Good luck