There is a batch convert option in Alley (Which is also muti-threaded so you can do 3 video's at a time). There's also an Adobe exporter feature added so you can batch convert in AME.
A Command line option like ffmpeg would be something the dev's would have to tackle, but for now, those 2 options listed will get your batch conversion started. I prefer Alley over AME because it's multi-threaded