HandBrakeBatch is a fully independent application which uses HandBrake video converter under the hood, and allows you to drag & drop a bunch of files at the same time, and convert them using any of the default HandBrake presets. With version 2.0, I have added the most requested feature: support for multiple audio languages and subtitles.
The application is Charityware (if you find the application useful, please go ahead and donate! I have selected some charities, but feel free to suggest more and I will consider adding them) and licensed under GPL (as HandBrake is). The source is available on github.com, and the complete application is available here. A wiki is also available on github, with additional information (release notes, requested features, etc.). If you find problems, please send me a message or add an issue on github.
Updated on Feb 03 2015