Most movie lovers dont want to mess with the directors original vision so personally I wouldnt cut away parts of the original picture just to fill the screen (or even worse, stretch it),that is almost going back to 4:3 TV's again. Almost all movies made for cinema is made in an aspect ratio greater than 16:9 (1,78) so black bars will be present from all sorts of sources (bluray, cable, sat.. whatever).
(only reason parts of the Dark Knight sometimes has 16:9 format is because some scenes were shot with IMAX equipment.)
But what you want is probably possible by reading the manual to "mplayer/mencoder" and playing with the "mencoder" options in the transcoding setting. But in my (not so humble
) opinion that is too much trouble and only depraves you of seeing the movie in the way it was meant to be seen...
(and that concludes todays rant)