Happy Feet has some interesting tips for keeping your shoes healthy after wet outings:

• Do not put them in the dryer and do not place them directly over a heater or too near a heat source.
• Remove the laces and open the tongue so the shoe can breathe. Remove the insoles so they dry outside of the shoes.
• Stuff newspaper into your wet shoes to help dry them out overnight.
• Before using them again, sprinkle a bit of baking soda powder into each shoe and again after using them.

Or you could go the overkill route: Get some overshoes. I have these mondo boots by Neos that look like something you’d take on a moonwalk. They add quite a bit of weight (especially when there’s mud and muck afoot), but think of it as resistance training. Best part: you just peel ’em off and toss in the trunk of your car when you’re done hiking, and you’ve got clean shoes to wear home (They will be a bit damp because there’s none of that sissified GorTex and you’re feet’ll sweat. But like I said, it’s a workout, right?).