EE Add-on Documentation Using Sphinx
I have a post planned on the new documentation from EllisLab but until then, read this tutorial from Exp:resso on how to document your CodeIgniter and EE add-ons using the same tool that EllisLab uses: Sphinx.
The beauty of using Sphinx is that you can write your documentation using ReStructuredText, a text format similar to MarkDown. You can then easily generate your docs in a variety of output formats, including HTML and PDF. It also helps to keep your content separate from design, and automatically handles repetitive tasks such as generating a table of contents / navigation, and linking between your documents.
The blog post walks you through the entire process of installing Sphinx and styling it like the official ExpressionEngine documentation.
Read the full tutorial: Documenting ExpressionEngine and CodeIgniter Add-ons