3DMJ have released a video with a bit of information about squatting and the knees going past the toes issue:http://www.youtube.com/watch?v=v_uWVg2_-ks
To summarize briefly, its ok for the toes to go over the knees....the issue is what breaks first between the knees and the hips to initiate the squatting motion.
If the knees break first the tendon running over the patela bears all the weight as you lower down (bad). If the hips break first then the load is transferred through the hips and glutes alleviating the strain on the knees.
Notice that regardless of whether you break at the hips or the knees first to initiate the movement, the position your knees end up in relative to your toes at the bottom of the squat is the same. It just seams to be an issue of how you get down there and what bears the load on the way down.
I would say you still don't want them to be way over your toes at the bottom as that will put alot of pressure on that tendon running over the top of the patela....but if you have long as femur bones then they may go over more than someone with shorter femur bones.