HandBrakeBatch can be used as an independent application. It uses HandBrake under the hood and allows you drag & drop multiple files at once and then convert them using any of HandBrake presets. Version 2.0 now includes the most requested feature: support of multiple audio languages and subtitles.
The application is called Charityware (if the application is useful to you, please consider donating! It is licensed under GPL (as HandBrake). Github has the source, and has the entire application. You can also find additional information on github (release notes, requests for features, etc.) in the Wiki. Send me a message if you have any problems. Add an issue to github.