The two worst things shoes have done to our feet have been to raise the heel and confine the toes. The elevated heel shifts weight forward, causing more weight to be taken up by the metatarsal heads; tightening the gastroc/soleus/achilles, and altering joint torques at the knees, hips and lower back. The confinement of the toes may be the biggest culprit to modern foot pain. Our toes were build to grip the ground and aid in propulsion; not to act as passive elements in the gait cycle. The smaller muscles of the foot that attach at the toes--the interossei and lumbricales eventually lose their strength over time, allowing (1) development of hammertoes and (2) significant body weight forced onto the metatarsal heads (ball of foot), helping to create many of the podiatric pathology I see daily. The weakening of these muscles is caused by modern shoes and the corresponding strengthening and tightening of the extensor muscles (top of foot) are caused by the need to lift a heavy shoe to clear the ground through the swing phase of the gait cycle.
A new minimalist shoe by Mizuno has just come out, highlighting the importance of the toes. Based on ancient Japanese design that allowed the toes to hang off the sandal, these minimalist running shoes aim to do the same thing. One arguement against them may be to question the direct pressure of the distal shoe cushioning on the metatarsal heads, but they do allow gripping action of the toes, which very well may allow for the development of stronger intrinsic foot muscles. It's an interesting design to say the least, and we'll see if traditional Japanese shoe design can help us out a little ;)