HandbrakePM can convert a lot of video files via the Handbrake Command Line Interface application (HandbrakeCLI). Simply drag and drop video files (not folders, only files) onto the icon or window and click the hammer-icon in the toolbar to convert your movies.
NEW
Found a way to reactivate the app after processing so it responds to mouse clicks again. Hopefully this solves the problem where the app would not come forward.
