well, free weights are... free.... weights..... basically they're barbells and dumbells, no machine to help you support or restrict movement, whereas machines/pulleys are where you use a machine to stabalize the movement and pulleys to lift the weight in a way that you normally wouldn't be able to, like doing pull-downs, if there were no pulley/machine, you wouldn't be able to do weighted pull-downs...
machines are good, but imho, free weights are better, they work the supporting muscles as well as the muscles you're trying to focus on. so rather than just working out your chest and tris when doing a chest press using a machine, you use all the stabalizing muscles in your upper body to keep the weight from swaying and stuff... creates a better network of muscles in your body, i guess you could say