The typical reason why the knees pop forward at the bottom is because most people do not know how to use their hamstrings to extend the hip (or as others have pointed out it could be just overly tight hamstrings). It is pretty foreign at first. A "Terribly Useful Block of Wood" will help you out immensely. The only way the hamstrings can be used to extend the hip is if the knee remains stationary. This means that the knees must come forward and stop after the first 1/3 to 1/2 of the descent. The knee can continue to flex as needed but the rest of the motion is in the hip. The TUBOW will give you a tactile response to let you know when your knees are forward far enough and if you are remaining in contact with the object for the rest of the descent and on the way back up. If you can maintain light contact with the object, meaning you are not pushing it with your knee, maintain your balance by leaning forward, maintain the weight on your heels, and maintain a tight natural lumbar curve with the chest up, then you have won most of the battle. When you do this right you will feel pressure/strain in the lower back... this is normal. Your hamstrings are trying to rock the pelvis posterially (rounding the back) and your back is fighting this. The rest are minor, albeit important, details that people tend to get right the first time.
Your stance should be just outside shoulder width. If you stand up straight and point your arms/hands straight at the ground, that is about where your heels need to be.
Most people who say they cant get low enough usually need to concentrate on pushing their knees out after the first 1/2 of the descent. If this doenst solve the issue then you should be doing the squat stretch and the hamstring stretch for 30seconds 3x/day as detailed in Starting Strength. It shouldnt take very long to get to parallel maybe a couple of weeks max.
