did the smell go away after a while?
do you usually run it on max/re-circulate?
has it been exceptionally humid?
if it went away, i wouldnt worry too much, if it is still smelling, it is probably mildew built up somewhere from the presence of too much moisture. a dead animal is also a possibility if the smell is still there, but it should dissipate in a few days, whereas mildew will probably never leave until it is treated.
edit: the moisture build up is usually in the evaporator, and running the fan w/o the ac on for a few minutes before you shut the car off can usually dry it out.
one more thing, if it smells like rotten eggs (sulfur) and not musty, it may be the catalytic converter gone bad...