I do nothing but free weights. I only have a bunch of dumb- curl- barbells and about 300kg of weights.
Off the top of my head, I prefer free weights over machines because...
* Getting the weights into position is already a small core workout. If you don't believe me get into bench press position with two 120lbs dumbells and get up again without dropping the weights. I've seen fit people that could not move free weights into position, weight which they could easily do on a machine. Thats not functional strength. Not cool.
I think thats a very important aspect, before you lift you have to get the weight into position, which is a small but important workout in itself.
There is a reason why so many people like machines - they make lifting easier. But in the world of fitness easy isn't always good.
* Free weights works all the stabilizing muscles better and with free weights your core has to do stabilizing work
all the time no matter what workout you are doing. Biceps curls for example, on a machine you sit down, rest your elbows on a padding and do the curls. With free weights you stand up and do curls with a 100lbs barbell, your back, abs and core have lots of work to do to keep your upper body straight while you are actually working your
biceps.
People who only lift with machines can usually not lift nearly as much when using free weights or when having to move equally heavy objects outside the gym.
* Machines force you to do a certain range of motion, with some exercises its better for your body to find its own stance and position. Especially with shoulder exercises and exercise that put lots of stress on your wrists.
Not all machines have different grip options.
* Its plain cool to be able pick up really heavy weights and lift them without any machines, padding or seats. Let yourself grow a huge mustache and you'll feel like a super-manly strongman.
Free weight training is highly functional and minimalistic.
Machines have their place too, for example when you do max weight exercises, its much safer to do them with the aid of a machine to avoid injuries. Like Pako did when doing insanely heavy squats. I wouldn't do super heavy squats without two spotters or a machine either.