I really don't understand why most people in the Humanities insist on using Microsoft Word to write their material. Universities habituate their undergraduate humanities students to Word and they really ought to stop it. I recently got a shock to my anti-Word stance when I wrote an article and was looking to submit it to a journal that only takes MS Word format articles. The journal also had a really nasty custom citation format, which complicated it even further.
In the past I've written about using LaTeX and other tools to write my PhD. I start in Scrivener, and export to LaTeX for layout. LaTeX of course won't export to Word's .docx format without a lot of rigmarole. I needed another tool.
On the other hand Scrivener has excellent abilities to work with snippets of text, which are presented as index cards which you can rearrange – excellent for organising your thoughts and notes. Its only major defect is that it uses RTF underneath the hood to store your text. They suggest using Multimarkdown format (and have some built in tools to support it) but the underlying data is still saved in RTF replete with WYSIWYG markup. You have to fiddle with it in order to force it look like a plain text editor (e.g. set the font to Courier). The developers should just create a "plain text mode" which not only behaves like a plain text editor – it also stores the content as plain text. This one flaw prevents me from fully embracing Scrivener. Nowadays for me it's just an organisation tool I use when my writing needs to be extensively re-organised.
Instead I've fully embraced Markdown syntax in plain text files via a tool called Pandoc. This is a command-line tool that converts to and from many formats. It can convert Markdown to RTF, DOCX, HTML, LaTeX, or PDF (via LaTeX) among many others. Pandoc has saved my bacon! It also has some excellent markup extensions that support things like citations, and it can integrate with bibliography data like .bib files, via bibLaTeX coupled with custom-styled CSL citation formats that allow me to produce the desired citation style in all target formats. So I write in this Pandoc-extended Markdown format and export to LaTeX/PDF or Word or RTF as necessary. The plain text files that make up my thesis and article writing as version-controlled via git on github – not that you'll see my thesis there, as it's in a private repository, sorry!
My editor of choice is Sublime Text. It was BBEdit, which still sometimes gets used for some things. Sublime Text is easily extensible via Packages, and it's easy to program your own. I wouldn't fully recommend Sublime Text to a non-programmer though – even the preferences are just stored as files with JSON objects! I'm still running Pandoc on the command line at the moment rather than using one of the Pandoc integration packages in Sublime Text.
I also had a look at [Ullysses III]. However it doesn't really fully support academically-styled Markdown – it doesn't know how to do Pandoc's citations for example. Also it tends to default to write its files into Apple's iCloud, which means you can't get at them on the command line. Although you can import 'external' folders into it, it's much more of a tool for 'creative' writers who just need simple formatting in plain text rather than academics who need to do complex things with citations and maybe tables, diagrams, and LaTeX math snippets, which are important to people in physics, maths and computer science.
In short, I am quite happily using plain text files and Pandoc to organise all my writing needs. Plain text being plain text, I can easily switch tools to handle specific tasks which that tool is particularly better at. I can write my thesis on my iPad (and I frequently do, using a bluetooth keyboard, which makes a fantastic portable writing toolkit). I can reproduce any journal's custom citation format easily (and switch between them), and target whatever document format they prefer. I can still use LaTeX for its fantastic layout abilities which creates far nicer looking PDFs than Word ever can. And if anyone still requires it in Word format, I can send them that too. You'll find yourself having less nightmares than you will with Word doing weird things to your formatting, and more to the point, when you need to just write using plain text allows you get all those jumping Microsoft distractions and hideous "ribbon" menus out of the way and concentrate on just the thing you need to say.
Update: If this sound terribly technical, this is a sample of how to write in Pandoc/Markdown:
#The header of this text is easily readable# Writing in Pandoc is super-easy. Fire up your plain text editor (e.g. Notepad or TextEdit) and start writing now! A guide - this is in *italics*, this is **bold** and this has a footnote.[^footnote] Blank lines separate paragraphs.^[this is a pandoc-only inline footnote] [^footnote]: the 'footnote' reference text must be unique. Pandoc will auto-number it. The footnote text can be at the end of the document or after the paragraph, it doesn't matter. You can also create references as follows: [@ACitationReference1999 p. 1] says so. Pandoc will invoke your chosen bibliographic software to extract the reference and format the citation according to your chosen citation format.