Before I get into this I have to note that for most writing I try to keep things as simple as possible: I compose (using Vim, mostly) almost everything in plain text (using MultiMarkdown (see an example of Markdown and its output), converting to another format using Marked, orScrivener, or something even more geeky like Pandoc.
But my Holy Garil of Writing Workflow is to, as seamlessly as possible, move through all four of the funamendal writing stages:
BrainstormingOutlining and/or Mind MappingComposing with Scrivener and Multimarkdown (which I am falling in love with)Publishing, as needed, to various formats:MarkdownPDFMS Office or RTFHTML