Markdown Doclet is a replacement for the standard Sun Java Doclet that allows developers to use Markdown syntax in their Javadoc comments rather than embedding unreadable HTML. The advantage of Markdown is that the syntax allows for HTML to be passed through, allowing the Markdown doclet to be applied to any existing codebase which may contain HTML Javadoc comments. It also includes a patched version of UMLGraph which calls the Markdown Doclet instead of the Sun standard doclet. The doclet also writes a more modern stylesheet for more attractive Javadocs.
HyperSQL is like the doxygen program with Javadoc added, but for SQL. It hypermaps SQL views, packages, procedures, and functions to HTML source code listings, and it shows all the code locations where these are used. You can use JavaDoc-style comments for documentation and even embed UnitTests with them.