I'm sure there are a bunch of these for different purposes, and mine is nothing particularly new, but if you're looking for a way to automate encoding across variable inputs -- sources with different types or numbers of audio or subtitle tracks, etc. I've written a perl script that might help. It first analyzes the file with HandBrake and then calls HB again with a parameter set what will preserve all English audio and subtitles, fold in external SRT files, select an appropriate wrapper, and produce as the first audio track an AAC mix-down (while preserving the originals as higher-numbered tracks) for compatibility with low-feature playback devices.
It's up on github so I can easily publish updates:
https://github.com/profplump/Handbrake-CLI-Helper
I'm willing to provide some support for it -- just email me -- but if you don't know how to execute a perl script, or how to edit the script to point to your local HandBrakeCLI binary, this is probably not the tool for you.
HB-CLI Automation Tool
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