I've seen the idea fronted here and there that one should not allow the knee to extend past the toes when one is squatting or lunging because it will cause terrible things to happen to the knees. It may well be that one is less stable or balanced when the knee is extended that far, but there is nothing inherently dangerous about it. I don't think you need a source, as there is plenty of non-epidemiologic and common sense evidence to dispel this myth.
On the epidemiologic front, take a look at competitive Olympic-style weightlifters. Not only do they regularly assume full-squat positions in which the butt touches the achilles and the knees extend beyond the toes, but they do this at maximal ballistic speeds while slinging weights up to their shoulder or overhead with the addition of weights often well in excess of their body weight. Rates of knee injury and overall musculoskeletal injury in Olympic lifters are quite low... I think you will find quite low when compared to activities like football, group aerobics, or martial arts. Regrettably, I do not have the numbers available just now.
In terms of a common sense counterexample, have someone watch you get up out of a fairly low chair. Another way to approach it would be to experiment with low squatting with various foot positions. I think you will find that it is basically impossible to live and be active without jettisoning the idea that the knees should not extend beyond the toes.
In a way, there is a self-fulfilling prophetic logic to both the 90 degree myth and the knees-toes myth: if you deliberately make yourself less mobile and capable, you may well be less susceptible to aches and injuries. Hell, if you just lie in bed for the rest of your life, you'll probably never have another overuse problem...