The answer to your second question is that a free weight squat activates a higher percentage of muscle fibers per muscle group and a free weight squat requires the use of the posterior chain. In essence you are recruiting more muscles and more fiber, which in turn leads to more overall strength, etc...
The answer to your first question is not so simple. It would be incorrect to generalize and say that all free weight movements are better than all machines. However it is true that machines limit motion and add mechanical advantage. There are some muscles that are difficult to train due to gym restrictions and personal ability without machines. Machines also can add variety to train the different points of flexion for a muscle and help keep a person from getting burned out. That being said, I believe free weights offer more benifits and should be the staple of any workout. If your gym allows athletic lifts and powerlifts, then you can virtually train every aspect of your body. You will find that isolation is not always what you want in your training program (at least depending on your goals).
Hope this helps some.
Pax,
GS
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Speaking of philosophy, does anyone have a large object I can beat someone with?
When someone upsets you remember that it takes 42 muscles in your face to frown and only 4 to extend your arm and bitchslap the motherfucker upside the head
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