It happens to the best of us, David. A few things to try. One, is to make sure that you give your shoes a rest in between wearings. Ideally, you'd like to let them dry out fully before wearing again.
Cedar shoe trees help dry them out while freshening up in the odor department as well. And a pair of no-show socks will go a long way in preventing excessive sweating and smells.
Dust the shoes' insoles with some powder—anything from baking soda to baby powder, or specialty products from the likes of Gold Bond or Jack Black. Leave it in overnight and then dump out any excess before wearing them. The powder deodorizes the shoe and will keep future sweating to a minimum. Speaking of which, most of the smell is from bacteria feeding on sweat, much like the odor that starts emanating from unwashed denim. Which is why a few clever people have suggested an old selvedge trick: A few hours in the freezer to kill any bacteria. Think about the relief that'd bring on a muggy morning.