Ashland Dave talked about stinky shoes in his podcast of 26 September 2009 -- it was somewhere in the first 15 minutes of the podcast:
Running in the Center of the Universe
Stinky shoes are a real problem for me. I am a profuse sweater, so my shoes are always pretty soggy when I finish a run. They are relegated to a place on the porch when I finish running. They do all right until...
...until I run in the rain. For some reason, that seems to push them over the edge. Even though I take out the insoles and stuff the shoes with newspaper to get them to dry, getting them soaked that way seems to bring out the smell and make it permanent. I can wash them and, while it helps, they still stink. I've tried to spray them with Fabreeze and that works until I run again.
Any ideas would be greatly appreciated. Until I find a solution, though, Shoes, you stay outside!
Run well, y'all,