JSwiki

• 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.