Smith machine limits your movement to just up and down. When benching with the bar a lot of people have a slight arc in the up/down motion, ie bring the bar right down to an inch above your chest at say nipple level but when fully up and locked out the bar will be at shoulder level or some even directly above the face.

Depends what you are most comfortable with really I suppose. I prefer bench with the bar and try to keep my form as good as possible. I just dont feel comfortable with the Smith although when I used to do it now and again I could lift more weight.

I dont think one method returns more gains than the other if you use correct form, although I could be wrong