There are two kinds of TOC that go into making a Mobi file.
The first is the HTML TOC, which will give the clickable links inside the book. This can be incorporated into your regular text if your book is all in one file, or you can put it into a separate file, if you prefer.
Just write it up as a standard HTML document with links to the relevant places in your book, and list it in the OPF file the way that the
Kindle Publishing Guidelines say to do so.
The second kind of TOC which gives you the flickable chapter marks is created via the NCX, which is otherwise invisible when reading. This will be a separate file from your main text.
The KPGuidelines give you the info on how to structure and list this file in the OPF, but the
Wikipedia page on ePub will give you a nice example file for both, and links to the official specs if you want to know more detail.
To sum up, only three files are needed to provide both clickable and flickable TOC in Mobi:
- an HTML file with the sort of TOC that you'd expect to see at the front of a paper book
- an NCX file to provide the chapter markers
- and an OPF file to let the Mobi-generating software know about both of the above and include their info in the resulting file.
Hope this helps, and welcome to MobileRead!