[kroger]

It depends of the kind of book you are writing and what the final file format is. In the past I'd use LaTeX unconditionally, but I've been thinking about using Sphinx[1].

[1] http://sphinx.pocoo.org/

The two main approaches are to have the whole book in one big file or one chapter per file. I think that having one chapter per file is more flexible and that's the way I'd do today.

Another thing to keep in mind is if your book is going to have source code. Is it going to be highlighted? If so, in color or grayscale? Do you want to have a way to test automatically every code snippet so you don't ship the book with broken code examples?

Also, do you have images that need to be converted, say from inkscape to png or eps? Usually I use a makefile for things like that.