The best way to comment directly in the source code is using JSDoc, the JavaScript equivalent of JavaDoc.

To comment on the code, just insert specially formatted comment lines (starting with /** instead of /*) containing a description text and tags before each class, attribute or method. As in JavaDoc, there a several tags to describe the source code: @param, @return, @version and many more.
If you have included this comments, you have to run a perl script over the javascript files which creates a bunch of HTML files containing the information from your sources.

But be careful if you are commenting on private methods! In this example there will be no comment for _privateMethod():

/**
 * Description for this MyObject..
*/
function MyObject(){
 
/**
 * @param {object} myElement Description for myElement
 * @private
*/
  var _privateMethod = function(myElement){
    ;
  }
 
/**
 * @return {number} Answer to Life, the Universe, and Everything
*/
  this.publicMethod = function(){
    return 42;
  }
 
}

JSDoc does not support this way of defining private methods. You have to use this scheme: 

 
function MyObject(){
  function _privateMethod(){
    ;
  }
}