Sprinkle some bicarbonate of soda into the shoes. Leave overnight and then tip the bicarb out. It aborbs the smell leaving them fresh. Works with trainers too.
I use Scholl shoe spray, you can buy it from Boots or Scholl shoe shops, I find that really good, you'll need to open all of your windows in your house though, its strong! I have heard orange peel is pretty good as well!
Putting scrunched up newspaper inside (unless they're light coloured and it could rub off) and leaving it in at least overnight can help to absorb some of the smell.