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There are two aspects to this problem:
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1. Knowing the encoding of the source file: |app| tries to guess what character encoding your source files use, but often, this is impossible, so you need to tell it what encoding to use. This can be done in the GUI via the :guilabel:`Input character encoding` field in the :guilabel:`Look & Feel` section. The command-line tools all have an :option:`--input-encoding` option.
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2. When adding HTML files to |app|, you may need to tell |app| what encoding the files are in. To do this go to :guilabel:`Preferences->Advanced->Plugins->File Type plugins` and customize the HTML2Zip plugin, telling it what encoding your HTML files are in. Now when you add HTML files to |app| they will be correctly processed. HTML files from different sources often have different encodings, so you may have to change this setting repeatedly. A common encoding for many files from the web is ``cp1252`` and I would suggest you try that first. Note that when converting HTML files, leave the input encoding setting mentioned above blank. This is because the HTML2ZIP plugin automatically converts the HTML files to a standard encoding (utf-8).
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3. Embedding fonts: If you are generating an LRF file to read on your SONY Reader, you are limited by the fact that the Reader only supports a few non-English characters in the fonts it comes pre-loaded with. You can work around this problem by embedding a unicode-aware font that supports the character set your file uses into the LRF file. You should embed atleast a serif and a sans-serif font. Be aware that embedding fonts significantly slows down page-turn speed on the reader.
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What's the deal with Table of Contents in MOBI files?
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manual/faq.rst
