[This is part of a series on the tools I used to write my PhD. Check out the other parts here.]
Mellel is what I use for the final formatting of documents. It might be overkill for some, but in the case of my PhD, the extra features really saved me some time and headaches.
At first glance, there isn't much to distinguish it from something like Pages.app or Microsoft Word. Mellel is a word processor. It allows you to format how the text is presented on the page. The level of control over those decisions is what distinguishes Mellel over the free/default alternatives.
For example, styling formatting for certain types of text is easy in Mellel. Want to change the way all headings of a certain level are formatted? Mellel can do this. Want to manage the formatting of Arabic, Pashto and Dari text without worrying that things will come out the wrong direction? Mellel is designed to handle these right-to-left languages and scripts. Want to do things with bibliography formatting and scanning? Mellel plays well with Bookends and the other reference managers. Similarly with things like your Table of Contents: Mellel handles it all with style (literally!).
An alternative to Mellel is Nisus Writer Pro. As far as I can make out there isn't that much difference between the two. Mellel also has a version for iPad so you can work on documents on the go as well.