14 DAY TRIAL // Calibre (reviewed here) received an update today, to build 0.9.26. It expands the functionality of the ToC (Table of Contents). Various repairs are also on the list, one of them touching on the PDF Output component (generating page numbers causing links not to work).
Starting this build, the ToC Editor allows you to generate the table of contents from individual files available in the ebook. The functionality of this option applies to EPUB files that have chapters stored as individual files.
Furthermore, now it makes available the possibility to indent the current entry and you can use the context menu for various actions.
In the case of PDF Output, the developer added the option to use templates in order to create arbitrary headers and footers. The function is present in the conversion dialog, under PDF Output. The full list of modifications is available on this page.
Download Calibre for Windows; portable version here.
Download Calibre for Mac
Download Calibre for Linux