not sure whether its a good idea to alternate these, but i find it useful lol.
eg 3 days machine, 3 days free weights.

Well, generally, free weights are better for major complex exercises while machines could be better for isolated exercises.

Machines balance the weight for you, making it less of a complex move. The more the complex the movement is,  the more muscle groups are involved. Also, contrary to popular belief, some machines are more dangerous than free weights. They force your body into a stiff, unnatural movement patterns and puts more strain on the joints.

For example, I see people in my gym using Smith Machine to squat all the time. They think it's less dangerous. That could only be true if you DO NOT know the correct technique of squats. While it's true not being afraid of a 100 kg barbel falling on you is nice and all, If you can squat properly in terms of technique AND weight (you can't add 200kg when your limit is 120kg, you gotta be reasonable) then you shouldn't worry about that! I couldn't have explained it better than Mehdi:

10 Reasons Why Squatting In The Smith Machine Sucks
Also, machines are more of a structure work than function. I prefer to have more 'functional' muscles that would help me in sports. Weightlifting/powerlifting plus doing sports can get you a perfect body. Bodybuilding is generally bad for athletes because it can make you stiff, gives you 'structural' muscles that are not that functional and will only slow you down. Here are a couple of good reads:

Machines Or Free Weights: Structure Vs. Function!
Also, do not forget people like Arnold Schwarzenegger built all their muscles with nothing but free weights!

Seems like someone didn't really read my reply thoroughly. I said free weights are more complex while machines are more isolated, targeting specific-muscle groups more than free weights. Like Dorian said, if I want to focus more on the QUADS I'd do smith, when free weights squats focus a lot on the lower thigh muscles and lower back. Anyways, I'd rather build more functional muscles than structural muscles that will only hinder my athletic abilities.

Well I wouldn't listen to EVERYTHING someone on roids says... 

Uhm, did I? Nope. Not whatsoever. Mr O's deserve to be Mr O's because of their genetics and their training. All who compete in them however, use steroids and it is a fact that steroid users can get away with training styles that prove ineffective to the average natty. Just cuz it worked for them doesnt mean it works for someone who is not enhanced. I'm not saying EVERYTHING they say is not true or factual, I'm just saying that variables are variables and they are different for the average natural lifter. Am I saying Medhi iz teh better or whatever? No. I'm just saying that Yates is an IFBB Pro and Medhi is a natural. Sure his physique aint all that great but not everything he says is wrong either.

I'm no supporter of either. My basis is more towards factual science behind the lifts than 'what is wrong or right in broscience terms'. There's always truth to everything, but the hard part is figuring it out. I really like Jason Blaha's training ideology, for example.

Well I wouldn't listen to EVERYTHING someone on roids says...