Free Weight Exercises Train Movement Patterns
Whether you are talking about a sport or activities of daily living, you need to train movements and not just muscles if you want to get optimal carryover from your training to your activity. Training compound, multi-joint movements such as squatting, pushing and pulling through a natural range of motion has much better carryover to other activities, and will build muscular awareness, balance and stability in multiple planes of motion. You cannot do this with most machines.
Machines Don't Train Stabilizers
When you perform machine exercises, the resistance is supported by the machine. All you need to do is move the weight through its permanently set path of motion. None of the smaller stabilizer muscles are called upon to perform the movement and thus are never trained or activated. When you return to a functional movement in sport or daily activity, this can lead to inhibited performance and injury. As an example, if you go from doing chest presses on a machine and then try performing a free weight bench press, you will be weak and you will shake as soon as you get some weight in your hands because you will have no stabilizers.
Machines Have a Set Range of Motion
Machines are built with a set range of motion for whatever exercise they are designed for. Everybody has different body structures with different lever lengths, joint angles, etc. If you have a specific limitation or condition somewhere along your kinetic chain, performing an exercise on a machine with a set motion pattern that your body is not built for can do much more harm than good.
Free Weight Exercises Train a Maximal Amount of Muscle Simultaneously
This kind of ties in with the first point, but when you perform multi joint free motion exercises, you stimulate a maximal amount of muscle simultaneously. This is ideal for any activity carryover as well as for fat loss. This does not happen with most machines. For example, lets take a look at the leg extension machine. With this machine, you sit down and simply extend your knee, working your quadriceps muscles alone. Never in any situation will your quadriceps work completely alone. They need to work together with the many muscles of your hips and other areas of your legs and core. In addition, this exercise puts lots of unneeded stress on your knee joint; thus, unless you have healthy knees, its contraindicated for a lot of people. Finally, performing a single joint motion such as this will not release fat burning or muscle building hormones and will not force your body to work very hard.
The back extension machine pictured up top is another good example. Simply leaning back and extending your low back is doing nothing. Your back needs to work together with your glutes and hamstrings. Promoting extreme ranges of motion in flexion and extension in the spine without any motion in the hips like the machine pictured above does, actually contributes to pain and injury instead of protecting against it.
In conclusion, if you want to build the best body possible, finally get rid of pain, or improve your performance as much as possible, you HAVE to train with free weight exercises. Now, I am not saying that ALL machines are bad. There are different types and categories of machines and there are some that are good and some that have their place in certain programs. They just have to be selected appropriately and put into the right area of a program. Hopefully this clears up some of the misinformation some of you may have seen or heard.