First off, Mark Rippetoe is the man. His seminal book Starting Strength is the Bible for building strength through full body movements, primarily the squat.
Secondly, LoL at anyone who thinks deep squats are bad for you're knees. I'd be willing to bet that most of these people have never squatted more than 2 plates to depth in their life. And smith machines don't count.
The definition of parallel is when the crease of your hip (where you're thigh meets your hip) is level with the top of your knee. When you break parallel on the squat, the movement engages the hamstrings and gluts more, making it more of a hip dominant exercise than a quad dominated exercise. In fact, stopping above parallel is actually WORSE for you're knees because of the shearing forces placed on your knees in stopping and reversing the motion, rather than utilizing the stretch reflex that kicks in when you break parallel.
The depth standard for powerlifting competitions is that you must break parallel for the lift to count. There's no way that this would be the standard for squatting hundreds of pounds if it was bad for your knees. I know some people will point to the gear powerlifters use (squat suits, wraps, belts, etc.). The depth standard is the same for raw, unequipped powerlifters as well.
Also, look at the depth that olympic lifters hit when they clean and snatch. They are going way below parallel with, again, hundreds of pounds.
Squats are the best way to build total body strength. Pick up a copy of Rippetoe's book. It'll change your life. It did for me.