Scrivener is a word-processing program that differs from traditional software like Word in that it allows you to create your documents within what it calls "binders," including the parts of your draft, along with other notes, research, and more. For many people, what is most appealing about Scrivener is that it is built to explicitly recognize that we don't always write in a strictly linear fashion. You can easily jump between sections or reorder them, or even highlight sections that focus on a common topic and work on them all at once. Scrivener also allows you to open side-by-side windows so that you can write while looking at your notes or reference material, and it has functionality for keeping notes, tagging things, and far more. It has too many features to do justice to here, but if Scrivener sounds like an interesting way to write, explore some of the links below to learn more.
Scrivener is available on both Mac and PC. It is in a slightly awkward moment right now—version 3.0 is available for Mac, but PCs are still running an earlier version (but 3 for Windows is coming soon!). Right now, Scrivener for Mac is $49 ($41.65 for students and academics with an institutional affiliation) and $41.35 ($38.25) for Windows, with the promise that new users will get a free upgrade to Scrivener 3.0 when it is available. That cost is a one-time software download; small updates are free. Any major updates (which are rare) will come with a discount for existing users.
One other important note: Scrivener offers a 30-day free trial period. This is an especially good trial, because it only counts days in which you use the software as part of the 30 days, rather than 30 days straight. This gives you plenty of time to play with Scrivener, dive into its functionality and overcome the initial learning curve before you have to decide if it's right for you.
As mentioned above, Scrivener has A LOT of features. This is both good and bad—it is flexible and can be manipulated to serve your workflow, but it also can overwhelm new users, because there is a lot to take in at once. The good news, though, is that there is a robust forum and community of Scrivener users to offer advice and help, and Scrivener converts seem to stay loyal to the program. (Full disclosure: the writer of this entry has used Scrivener for almost 8 years!)
Scrivener is produced by the same company that makes Scapple, and if you like using them both you'll be happy to know that they work well together—you can even drag Scapple notes into Scrivener.
One caveat, though: Scrivener does not work easily with Zotero (there is theoretically a work around, but I cannot testify to its effectiveness). My solution is just to export my work to Word when it's getting to be a more complete draft, and then use Zotero to update the footnotes there.