I use Scrivener for most of my writing. I see some have touched on it already, but I think Scrivener deserves an explanation, because it is truly a great piece of software (and even though it isn't free, the price isn't that hefty, either).
Scrivener is a writing tool that is great whether you write short stories, novels, scripts and even essays or scientific articles. One of the big features of scrivener is that you can organize the project however you want, by chapter, by scene, anything. In the end, when you are ready to export, it all comes together into a single text.
You can append all the research files you need to the project, for fast in-application reference. You can add labels, status and even your own meta-data to separate pieces of text, so you have a say on how it all will be sorted.
You can have two parts of text viewed side-by-side, for comparison or reference, you can even have that second chapter in the same window where you are just writing chapter nineteen, because their events are closely linked - all without any copy-pasting.
I find Scrivener a very streamlined piece of software for writers and am happy with it. I use it for almost all my writing.