The answer that I came up with while searching
It turns out it's fairly common problem, which in the vast majority of instances stems from using the HVAC "recirculation" mode. In this mode--put as an option on cars so that if you are stopped behind a bus the AC won't suck in the noxious exhaust fumes--the system doesn't draw in outside air, but recirculates the air in the car.
If you keep the recirculation button on for a long period of time it causes condensation build up in the system, particularly the filter, which produces a nasty smelling mold. I have heard horror stories that once the mold builds up, you have to replace the entire system.
In my case, I simply remembered to keep the recirculation button off, and it went away in a few days. I might also have run the car one night with the heat on to help dry it out and kill any molds. In any case, the problem has never returned.
edit. Or a mouldy marathon bar in the cubby