http://www.drscholls.com/drscholls/conditions/footodorperspiration.jsp She got a foot fetish you're worried about?
do not, I repeat DO NOT try to freshen them up with any fragrances, I'm sure they would not mix well. Buy new shoes and also buy a fresh (baby powder) in-sole, they are sold at academy for 3 bucks.
You can also use color safe bleach to clean it out and get rid of the smell. I've used this trick with my teenage son on multiple occasions.
Buy new shoes and always wear socks. Buy some new socks while you're at it. Most importantly wash your damn feet and make sure they're dry (especially in between the toes) after you get out of the shower.
Unless they're Sperry's you should definitely start wearing socks. If your feet sweat at all, your shoes will stink up after literally a few weeks without socks. You can get some stuff that you can spray or powder on, but start wearing socks.
Make sure your socks are long enough too. Don't wear socks that do not cover the lowest part of your ankle.