afaik - it's a good idea to keep your knees and toes in the same line, to prevent force acting across rather than down the knee joint. This is what the PL folks at my gym told me - they said I was pointing my toes out too much and my knees were not in line, and this would wreck my knees...
Toe position is not a real issue as far as torque on the knee. I really don't think, there is much research that shows how a squat can damage the knee. I think most knee injuries that occur while squatting are due to excessive loads that the individual should not be handling.