This was one of the most requested features for HandBrakeBatch: support for files with multiple audio languages, and subtitles. Finally I got around it and tried to implement it in the simplest possible way.
Have a look at the screenshot at the top of the post, the idea is very simple: you configure your language preferences once, and they are respected for all movies. For audio, you can select to maintain all languages during the conversion, or just your favorite (if available). For subtitles, you can also decide not to include any. On the top of that, the program is now able to detect and display the available audio languages and subtitles when you add the video files.
I haven't released the new version yet, but all the code is on github, on a separate branch. Feel free to download the code and play with it! If you are not familiar with compiling Mac applications, drop me a note and I will send you a test version, or wait till the weekend when I will have time to do some more serious testing and publish version 2.0.