I used to write my documents in Lyx too but spreading the tool amongst my colleagues involved a lot of evangelism. Markdown is a backend storage easier to adopt as developers are used to it (stackoverflow, github) but it produces output for the web : no pagination, header/footer, etc. Throw pandoc+tex template into the mix, and it starts to get really interesting : a quickly hacked markdown file transforms into nice pdf will all needed attributes. But why stop there? Now that you have a build process, move it to a server and add some hooks to injects traceability infos (author, last edit date, commit hash...) into the generated document, etc...

I went down this road, and it works surprisingly well. If you're trialling different solution for writing technical developer documentation, see a more precise description of the workflow that I pushed on my blog yesterday: http://kray.me/pro/doclegit-git-documentation-server/ (sorry for the copy quality, english not my first langage, corrections by mail are welcomed)