Structure
The next thing to look at is the overall structure of the document. You can
visualize a Markdown document as an outline, with different sections and
different levels within those sections. Based on your output format, these can
be used to generate headers, or sections, or even chapters. It's all based on
what tools you use to process the XHTML output.
Even within the XHTML document, however, you can make use of this structure to
allow easy navigation within the document. You can link directly to the
Introduction (and to when using LaTeX), for instance. And
if you are creating a PDF, it will contain a hierarchy of section names that
you can use to allow easy navigation, if your PDF reader supports this
function.