Like the PP suggested: Rotate how often you wear certain shoes and wear fresh/clean socks every day plus make sure they air out completely. For instance I have 2 pairs of dress shoes in the winter and I rotate wearing them every other day. Instead of wool - I like bamboo as an option especially for dress socks.
During the winter I have this problem because my feet sweat, bacteria builds/grows and hence transferrance. The summer I rarely have this problem as my feet are often bare or in flip-flops.
Its awful! I can smell my feet from like 100 yds in the winter when I take off my shoes
In addition to the BS - I would also mix in a bit of TeaTree Oil as that has antibacterial properties and might give your shoes a freshening up.