As far as I know, there's no difference in the outcome. Opacity is handled by most browsers through hardware and I would imagine the filter method does the same. I would hope they are handled the same because it would seem wasteful to have two methods that do the same thing.

Somewhat useless thought, opacity and the opacity filter can be combined on the same element. If one is set to zero it makes the other irrelevant. If one is set to 100% then it makes itself irrelevant.