There is no easy answer for this. The debate will continue forever.
Many machines do allow independent movement of the limbs, that's not really an issue any more. Even the highly marketed home gyms, Bowflex, Soloflex, and Total Gym have this feature.
Free Weights have the advantage of not restricting the range of motion. Meaning that your natural movement during an exercise is not impeeded. That will alow you to use proper form to prevent injury and train the targeted muscles properly. The downside is that also allows the exact opposite to happen also. It is easier to do the exercise incorrectly with free weights.
Machines tend to lock you into doing it their way. This would not be bad if the machine was built just for you, and not for any body of any size and weight. Machines made for a specific exercise in most cases compare well to free weights for ROM. All purpose machines generally do not compare well to free weights for ROM as they are built to a "one size fits all" format.
The debate will rage on because there is no fair way to measure strength gains with the two systems. Exercise specific training will generally provide the best results. If the test is free weight benching, then of course a guy that trains on a machine is going to bench less on that test than if he had trained on free weights, the reverse would be true also on most of the newer machines.