Do you know an easy way to freshen shoes? Newspaper!
Crumble up some paper and stick it in your shoes. Let sit a few hours or overnight. The paper will absorb odors.
This is great for shoes that you can't run through the washer.
And... if you're worried about the newsprint marking your shoes, just purchase newsprint in pads at an art supply store (very inexpensive). It's newspaper without the print!