If your boots are smelling less than new, here are a few suggestions to freshen them up:
Try using either an anti-microbial or charcoal based insert, like Odor Eaters, to combat the smell.
Sprinkle the inside of your boots with baking soda and let it sit/neutralize overnight. Shake your boots out before putting them on.
In the same way that Dryel or fabric softener sheets wipe out light body odor, they can also be tucked into shoes to freshen them up over night. (Make sure to put them in the boot right after you take them off so they are still warm.)