I'll probably lose some nerd cred: I do most of my writing in MS word, I find it easier to cut and paste and add footnotes and section headers. And then I use Pandoc to convert the docx into the format I want, usually HTML*. I used to do markdown in vim but I found that for most of what I do I prefer word. I do write code in vim...
* I use this css file when converting: https://gist.github.com/killercup/5917178