* [Dox](http://visionmedia.github.com/dox/)
* [JsDoc Toolkit](http://code.google.com/p/jsdoc-toolkit/)
* [jsDuck](https://github.com/senchalabs/jsduck) - Simple JavaScript Duckumentation generator.
* [docco.coffee](http://jashkenas.github.com/docco/) - Even though primarily written for CoffeeScript, works with JavaScript too apparently.
* [docco-husky](https://github.com/mbrevoort/docco-husky) - More features than docco.
* [Sphinx](http://sphinx.pocoo.org/domains.html#the-javascript-domain) - Uses ReST syntax by default. Supports Python the best but it's adequate for other languages too. No automatic generation based on source, though.
* [YUIDoc](https://github.com/yui/yuidoc)
* [doctor](https://github.com/jdeal/doctor) - A documentation parser built around an AST parser.  Need to have a bit more of a look at it, but it looks pretty interesting.
* [dr.js](https://github.com/DmitryBaranovskiy/dr.js)
* [joDoc](https://github.com/davebalmer/joDoc) & [jodoc-js](https://github.com/azakus/jodoc-js)
* [AutoObjectDocumentation](https://github.com/vladocar/AutoObjectDocumentation)
* [NDoc](https://github.com/nodeca/ndoc) - Based on PDoc
* [DocumentUp](http://documentup.com/)
* [mdoc](https://github.com/millermedeiros/mdoc) - Generates documentation based on external markdown files.

## Articles

* [Let's Make a Framework: JSDoc](http://dailyjs.com/2011/01/20/framework-part-47/) - Despite the name this is an article that walks you through the process of using dox (see above) for generating your API documentation.  __NOTE__: The article does use an older version of dox that generates HTML output rather then the current version which generates JSON that can be passed to a templating engine.
* [Inline documentation, why I’m ditching it](http://blog.millermedeiros.com/inline-documentation-why-im-ditching-it/) - Explains advantages and disadvantages of inline and external documentations.