Free weights allow you to perform a much wider variety of exercises, they allow you to lift in your own natural range of motion, they are easy to scale, and they help build your stabilizing core strength.
Because they are not connected to any fixed range of motion, you can use free weights to do just about any possible exercise. These include squats, deadlifts, presses, cleans, curls etc.
Free weights allow you to use your own natural range of motion. Just take a look at an exercise as basic as the squat.
You will not find two people who will squat exactly the same.