HandBrake can include chapter markers when you use the MP4 or MKV file formats. These will be placed at the same point where the chapter breaks are on the DVD or in a source MP4 or MKV file.
Using Chapter Markers
In the main window, click on the Chapters tabs. Check the box next to "Create chapter markers" to enable the feature.
By default, the chapters are named "Chapter 1", "Chapter 2", etc. However, beneath the checkbox is a table listing the chapter numbers and titles. If you wish, you can give the chapters distinctive names by typing them in there.
The Mac and Linux GUI's will retain chapter names if the source file has them when re-encoding a file. (This will be added to the Windows GUI and CLI at a later date.)
Importing Chapter Names
You can import chapter names from a csv file. There is "Import" and "Export" buttons on the "Chapters" tab that allow for a csv file to be loaded.
The format of the csv file should be as follows. (Special characters should be escaped)
1,Chapter Name 2,Chapter 2 Name 3,Chapter 3 Name ....
Note: HandBrake can not create chapters if they don't already exist in the source file. You can only name the existing chapters.
Note2: You can also export the current chapter names to a csv file for later use.