For those of you who like science, and for things to be researched, here is an interesting paper recently published:

http://www.pmrjournal.org/article/S1934-1482%2809%2901367-7/fulltext

If you like your results condensed:

Results

Increased joint torques at the hip, knee, and ankle were observed with running shoes compared with running barefoot. Disproportionately large increases were observed in the hip internal rotation torque and in the knee flexion and knee varus torques. An average 54% increase in the hip internal rotation torque, a 36% increase in knee flexion torque, and a 38% increase in knee varus torque were measured when running in running shoes compared with barefoot.

Conclusions

The findings at the knee suggest relatively greater pressures at anatomical sites that are typically more prone to knee osteoarthritis, the medial and patellofemoral compartments. It is important to note the limitations of these findings and of current 3-dimensional gait analysis in general, that only resultant joint torques were assessed. It is unknown to what extent actual joint contact forces could be affected by compliance that a shoe might provide, a potentially valuable design characteristic that may offset the observed increases in joint torques.