I wouldn't use machines much if I had a shoulder or joint injury. The machines don't really allow you to work around an injury. They would more likely force you to "work through" the injury, which won't help the healing process.
Machines follow a fixed path. Free weights will allow you to manipulate the path and give you more of a realistic crossover from the gym to your daily life. Rarely do we come close to duplicating machine movements in our daily multi-directional/dimensional lives.
That said, if you are dealing with a joint injury, experiment with exercises. Find exercises that do not cause pain during the R.O.M. If you feel pain (the wrong kind, not lactic acid kind)-- get rid of the exercise.
It may take a while to find what works for you without hurting you and still allowing you to work the muscles efficiently.
I personally like to incorporate a lot of triceps into my chest routine. I will always go for closer grips with dips and barbells. If I want to isolate the chest, I will use dumbell flyes or pulley flyes.