Basically today there's two formats. Literal formats like PDF and MS Word documents, and flowable formats like HTML, ePub, etc. plus things like Markdown.
After that it's proprietary extensions such as DRM etc.
The flowable formats are text mostly and work well on a wide variety of readers and sizes. They also tend to be very portable and convertible from one to another. These are very nice as readers can change readers, change font sizes, screen sizes, font styles, etc.
ePub is essentially HTML with metadata, as much a "book" format as a page format. I have an ePub book on my phone, it has chapters, table of contents, etc. My phone tells me how many pages are left in the chapters, and what page I'm on in the book, but I and tweak the font size whenever I want. For my current book, I'm on page 1798 of 3174 pages. Mind, this is a generic several 100 page trade paperback book. It's just a zillion pages because of my font size and screen size.
PDF is designed for perfect copies. It's very important for graphic and layout heavy work. Rather than flowing the text to fit the screen, you zoom in and out until you can see what you want to see comfortably. Obviously most game materials are PDF as they tend to be graphic and table heavy. Plus legacy stuff is just scanned works from paper, which is the "lowest" form of electronic publishing, in my eye. But we take what we can get. I'd much prefer pure PDF in those cases, simply because the size of the scanned books is so enormous compared to pure PDF works. That's just impossible with legacy works, especially without the master documents.
As an author, format preference should not be much of an issue outside of the initial decision: are you doing a flowing work (i.e. generic book filled with text), or something layout heavy like PDF.
Because these decisions dictate your creation process and your overall design.
If you're just doing text, you can use anything structural. Word, OpenOffice, HTML, had coded XML, Markup, Troff. Anything that puts basic structure in to your raw text is translatable to pretty much anything else today. You can start in Word and end up in ePub easily. There's some pipeline somewhere that will take from your source form to some delivery format.
PDF is what it is. You start with ANY format, lay it out, and turn it in to literal PDF pages. That's on you as the author and the authoring tool suite. Again, Word -> PDF is trivial. So is HTML to PDF, etc. TeX, Troff, DocBook, other typesetting toolsets. More advanced PDF has nice things like inner links (like TOC to chapters, etc.). But PDF also offers you the ability to just "make it like this". Scan in a sketch from a napkin, plonk it in a PDF and "done". Obviously there is an entire industry around converting text in to laid out PDF files.
In the end, as a base lingua franca, MS Word is obviously VERY well supported. A lot of folks whine and complain about it, it has its issues. But there's lots of ways to work around all of those issues. I think Word requires discipline to get the structure in to it that any large document should have, because it's so easy to enter stuff in an unstructured way. It blurs the lines between semantic markup and layout, supporting both interchangeably, making it perhaps a bit too easy to mix them up.
But it's an easy way to do mass entry and get the stuff from the soft matter of your brain in to the hard matter of tangible, manageable digital assets. You can always reorganize it later. It's gotta be better than Bic pens and legal pads.
In the end, once you've may the "literal" PDF vs "flowing" text decision, whatever you start with can get you where you're going. The most important thing, is to get started creating. The tooling will work itself out later.