what free weights do as opposed to machines will work your stabilizer muscles, from that you won't get noticably bigger but you will have what I call "real world strenght", like if you were to lift a table over your head in real life, you would need thoes stabilizer muscles so you don't fall over and your able to control large objects. IE: you might notice on a machine you can squat 350IBS but when you do free weight squat it might only be around 290IBS cause your about to fall over or whatever, well thats a common problem for people who use machines to start with and then never switch over the free weights. does that make sence?
This is one of the main reasions for free weights.