MEncoder has many video and audio filters that HandBrake still lacks, and it's somewhat more tweakable through the command line. MPlayer/MEncoder has gained a lot of functionality during a decade of development and many talented people have worked on it, along with FFmpeg. However, MEncoder is built for AVI output and it would probably need to be redesigned to fully support modern containers. I expect MEncoder to be replaced by ffmpeg and other libav* frontends as soon as libavfilter gets committed to mainline FFmpeg and some useful MEncoder or AviSynth filters are ported to it. HandBrake(CLI) has lots of potential too, and it's delightfully easy to use.
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