I haven't tried it, but mkvmerge has a cropping parameter. You can specify different values for each edge.
I recall that HandBrake does, too, so it would be a matter of whether you want to recompress the video or not. (By default, Handbrake samples the stream to detect the black bars and crops them in the output, but you can override that. Obviously for a title with varying aspect ratio you'd want to check that autocropping feature carefully).