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.
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.