Then, smell-proof the shoes. Charcoal insoles such as Odor Eaters ($3 each) go a long way toward vacuuming up bad smells, thanks to the charcoal (an odor neutralizer) and baking soda (which absorbs odors). Use one for a few weeks, then replace.
The shoes themselves can be handled several ways. There are odor-killing sprays that are extremely effectiveFebreeze is an excellent one. Spray a little in each shoe, and the odor literally goes away. In most cases, it's also OK to rinse the shoes out (especially hiking boots) with a little warm water. This will help cut the sweat smells, and also prolong the shoes' lives by washing out the acid that sweat contains. I wouldn't recommend this for dress shoes, but most footwear can take it. I wash tennis-type shoes in the washing machine, and they come out fine.
So there you go. Good luck, and I hope never to run into your shoes. Anywhere.