the best way I've found is Quicktime Pro. Open your movie and choose Edit->Get Movie Properties (command-j). select the video track on the left and 'mask' on the right. then choose a black and white image file where black is where you want the movie and white is what you want cut. Ok, so it's not the best way, but it's the one people are most comfortable with, and you don't have to re-encode the video to do it. Other ways I found were Media Cleaner (under which it might be possible to not re-encode, I don't know), mediapipe, and something called Hipflics (I think)
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