From CommonJS Spec Wiki
A major output of CommonJS will be an API specification and possibly some user docs to help people get started with a CommonJS-compatible platform.
- http://code.google.com/p/jsdoc-toolkit/ (requires Java)
- Ejscript has a javadoc style doc generator called ejsmod. This doc, was generated with ejsmod.
- http://scriptdoc.org/ (no public tooling)
- http://www.naturaldocs.org/ (requires Perl)
- Code Illumionated uses an approach with nice typography to document code.
- Sphinx is a Python-based tool for building documentation packages based on ReStructured Text files. It can generate HTML and PDF. Paver has support for Sphinx to be able to maintain example code separate from the documentation files.