Machine can work all the muscle , but i guess the big diference between machine and free weight, is the stability.

The concentration for the stability when using free weight, force you to control all of your muscles, and gives you tension. This will make your muscle to work under more tension, rather than using the machine.
I guess this is the big diference, so we can easily say that free weight is better for endurence of the muscle, and i can force it to grow a bit bigger than using a machine