I used to have severe problems with my feet on long rides. If you do too, here are some things you might try:
1) Move your cleats back. The numbness is caused by nerves being compressed as you pedal. By moving the cleats back, you're getting some of the pressure off the balls of your feet. My cleats are all the way back; I've heard of some riders who drilled out there shoes so they could get they even farther back.
2) Use some orthotics (Spenco or equivalent). I had some success with off-the-shelf orthotics, but I had more success with custom ones. (John Hughes suggested a place in Denver, the Custom Foot I believe, that made me some great ones!)
3) Use shoes with a large toe box (I've found Carnacs wonderful!)
4) Carry a golf ball with you -- if your feet are hurting, get off the bike and roll your feet over the golf ball. It feels wonderful and you'll be ready to go again. (Tip was from a massage therapist on BAM.)