One of the "common" (heh) solutions is to use org-babel to have a "literate programming" version of your .emacs that you then weave/tangle into the real .emacs
Personally, I've tried this approach with some smallish programming projects and literate programming has to be a good fit for your way of coding. Since I'm quite a big tester-rewriter, LP is a heavy chore. Of course, I'd probably get better doing it more often.
They seem to imply that no weave/tangle would be necessary with Outshine. At least I assume that's how it would work with the outline headings 'outcommented in the comment syntax of the major-mode language'.
I've seen org mode init.el files using babel, I honestly really can't see the benefit of literate programming in this way. It makes debugging so much harder than it need be.
Personally, I've tried this approach with some smallish programming projects and literate programming has to be a good fit for your way of coding. Since I'm quite a big tester-rewriter, LP is a heavy chore. Of course, I'd probably get better doing it more often.