I really like the writing tool, Scrivener. I finished my first novel, The Murk Beneath (not published… yet!), using it and it was just fantastic. I only used a fraction of its features, but one of the big ones is being able to organise chapters and the scenes within chapters. Others include the performance as the overall word count ticks over 50,000 – Word just creaks and finding your way around from chapter to chapter is a pain; not an issue with Scrivener, which treats a book / thesis like it’s a filesystem.
My thoughts are turning to the larger thesis writing part of my PhD. It’s very early days, but I can at times be a prolific writer, so why not get some drafts down on virtual paper even at this stage? My main worry was citations and the bibliography. There is no native integration between Scrivener and my preferred bibliography management tool, Zotero. Help was at hand from this blog post. Zotero’s RTF (and ODT) scan tool works, plain and simple. The only minor drawback is not being able to click on a little icon and start typing a name or a title, like you can with the LibreOffice and Word plugins. Otherwise, though, the “Scannable Cite” works very well; it’s very straightforward to add a minus in front of the author to suppress it, and also to add some custom text (e.g. adding the word “see” before the citation within the brackets).
I think over the course of my PhD, the combination of Scrivener and Zotero will save me weeks of effort.