Documentation Tools

• Dox
• JsDoc Toolkit
• jsDuck - Simple JavaScript Duckumentation generator.
• docco.coffee - Even though primarily written for CoffeeScript, works with JavaScript too apparently.
• docco-husky - More features than docco.
• Sphinx - 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
• 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
• joDoc & jodoc-js
• AutoObjectDocumentation
• NDoc - Based on PDoc
• DocumentUp
• mdoc - Generates documentation based on external markdown files.

Articles

• Let's Make a Framework: JSDoc - 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 - Explains advantages and disadvantages of inline and external documentations.