Baking soda is going to be your bestie when it comes to removing odors. Either sprinkle a cup of it into the washing machine when you put your shoes in or add to your hand-wash cleaning solution before you tackle your insoles to get the best use out of its de-stinking power.
If you're working with an especially smelly pair of athletic shoes, you can also pre-treat by sprinkling some inside your shoes and leaving overnight before you start the cleaning process.