JSDoc is a port of JavaDoc. So basically the documentation assumes classical OOP and that’s not suited to JavaScript.
Personally I would recommend using docco to annotate your source code. Examples of it can be found for underscore, backbone, docco.
A good alternative to docco is groc
As for an actual API documentation, I personally find auto generated documentation from comments just does not work for JavaScript and recommend you hand-write your API documentation.
Examples would be underscore API, Express API, nodejs API, socket.io docs
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