When Chase and I were training last year, we talked with a personal trainer who works for the local university's sports teams. He said that he recommends that athletes strengthen the muscles in their feet by doing certain exercises -- it helps keep your feet from hurting as much at the end of the day.
There were two specific exercises that he recommended. One was to put a towel on the floor in front of you while you're sitting on a chair. Then you put your bare feet on the edge of the towel closest to you, and begin to bunch it up with your toes, pulling the towel toward you until you get to the other side. When you finish, put the towel back in its original position and start over. It's an easy one that you can do while watching TV, surfing the Internet, whatever.
Also, he said you could dump a bunch of marbles on the floor and pick them up with your toes and drop them in a bowl. Both exercises strengthen the various muscles and tendons through your feet; that way, when you start using those muscles on the trail, you've already gotten them in shape.