What's the difference of FaceTime App that came installed in my Retina Macbook Pro and the one that is in Mac App Store for $0.99?
FaceTime in the App Store is really only meant for users of 10.6 Snow Leopard.  As of 10.7 Lion, FaceTime comes pre-installed.

I'm not sure why Apple was charging for FaceTime in the first place.  Perhaps just testing the Apple Store sales model.