Here's a study(pdf) that compared barefoot walking versus walking in shoes in subjects with knee osteoarthritis. The study "observed relative load reductions of nearly 12% at the knee and 4–11% at the hip merely by walking barefoot."
Also, the authors are speculating two ways in which modern shoes can be bad for the knees:
"Thus, it is possible that soles of modern shoes may increase joint torques compared with the flexible movement of a bare foot. A final explanation of the biomechanical advantages of barefoot walking may be attributed to increased proprioceptive input from skin contact with the ground compared with an insulated foot contacting the ground."
