I write my personal stuff in reStructuredText, which is like Markdown but with more processing possibilities and more extensible.
When it comes to professional stuff, depending on the size of the project, I use reStructuredText or DocBook.
DocBook is a must when complex stuff (like cross-references, recursive file inclusion...) is involved, and XML processing enables many fancy features, and output to many formats.
reStructuredText documents can be converted to DocBook, so it's possible to use a master DocBook document and rst fragments.
rst is definitely a plus for straight reading, collaborative edition and SCM.
DocBook is not as painful as binary files, but XML edition, diffs and merges is not as trivial as text chunks.
Then I use LaTeX for stuff with too many formulas, or stuff that really needs to look pretty.
But I dislike that there is no real separation between structure and looks of the document.
Also, LaTeX is harder to process and slower to compile.
DocBook or reStructuredText toolchains can process chunks of math code in LaTeX syntax, which is a nice tradeoff.
In all cases, writing non-trivial documents is easier when a good build system is used.
What I like most is the ability to share external resources (chunks of text, generated data, images, generated images,