I always try and flex my feet inside my shoes when I'm riding:

I'll curl my toes under and then splay them out as far apart as my shoes allow. I have real problems with my feet also, and it seems to be worse this year than last but that seems to help. Sometimes after a really long ride, I'll stretch and flex my feet just like I do my calf and thigh muscles. You might also try massageing your feet after a ride - see if that helps any.