Markup or WYSIWYG, that is the question. I've done it both ways. In my academic life, I wrote extensively using markup languages, including runoff, Scribe, and LaTeX. The editing itself was done using Emacs (the One True Text Editor). I've also done a lot of writing using WYSIWYG systems, primarily FrameMaker. WYSIWYG is better.
It's better for two reasons, but before I get to those, I have to address the markup bigots who argue that WYSIWYG editing mixes structure identification (e.g., "this is a subsection") with presentation decisions (e.g., "subsections should be in 11 point bold Palatino and numbered n.m"), a situation sometimes derided as WYSIAYG ("What You See is All You've Got"). Sure, people can do this, but paragraph and character formats (as FrameMaker calls them) or styles (as Microsoft Word and OpenOffice Writer do) also make it possible to separate structure and presentation, and anybody writing something as long as a book will soon learn to do so. There's no dichotomy between WYSIWYG editing and separating structure and presentation.
I should also mention that I generally produce camera-ready copy for my books. That means I'm making most of the decisions about presentation myself: page layout, font choices, all that fun stuff. I've observed elsewhere that preparing camera-ready copy is probably not a good use of an author's time (scroll down to "Typeset"), but I have my reasons for doing it (or at least most of it), so ignoring the details of what things look like is not a practical option for me.
WYSIWYG authoring is better than markup-based authoring for two reasons. The first is latency in error detection. Suppose I want to specify that a paragraph is a second-level bullet point. With a WYSIWYG system, if I select the wrong paragraph or I don't specify a second-level bullet, I see the result of my mistake immediately, and I can correct it without further ado. With markup, I don't notice that I've done something wrong until I submit my document to the document formatting engine and look at its output. Call me a renegade, but I don't enjoy finding out several minutes after failing to close an italicized (er, excuse me, I mean emphasized) section of text that my entire document is now in italics. I'd rather see the problem the instant I specify that something is to be italicized/emphasized.
The second reason I prefer WYSIWYG editing is that what I see on my screen matches what I see on paper. This is important when editing. Having printed a section or chapter and annotated the hardcopy with changes to be made, if I need to reword a sentence at the end of page 2, I want to go to the end of page 2 on my screen and start editing. With WYSIWYG, I can. With markup, what I see in Emacs bears no resemblance to what I see on paper, so before I can do my editing, I have to search for a phrase in the text near where I want to edit, then map what I see on the screen to what I see on the paper. Only then can I start editing. It's primitive and a waste of my time.
When looking for authoring software, then, I really want a WYSIWYG system. Unfortunately, I'm not happy with my options. I run Windows (so sue me), so I need something that runs on that platform. I've written my books since 1992 using FrameMaker, and let me just say that I hate it. I don't really know Microsoft Word, but I've heard enough bad things about it to consider it a low-percentage option, and my limited experience with it reminds me of C++: you can do pretty much anything, but almost everything is complicated by the fact that features interact in ways that make sense only if you understand absolutely everything. I wanted to use OpenOffice Writer, but I wrote an article using it, and that experience demonstrated that Writer just isn't up to what I want to do. (Cross referencing was painful, and PDF output was essentially nondeterministic when the layout included floating display elements like figures, listings, and tables.)
I've recently been looking at WYSIWYG XML editors supporting DocBook, but since one of the advantages of DocBook is that it can be transformed for display on different output devices (something I definitely want), I began to realize that the meaning of WYSIWYG is less clear when you'll be "getting" different things for different output devices. Presumably this an issue familiar to web designers who (properly) employ "liquid layout," i.e., allow line breaks to be determined dynamically, because that means that the appearance of their web pages is affected by the width of the window in which it is displayed -- something over which they have no control.
I find myself seeking a WYSIWYG editing interface for a document that may be formatted for several different output devices with varying capabilities and characteristics (e.g., font selection, support for color, physical size, etc.). What do you think I should do?