I have encountered this issue as well. I am now writing documentation for angularjs codes through jsdoc comments like this:
1.Make a blank .js file with the following comment:
 /**
  * @namespace angular_module
  */
This will create a separate html in the generated documentation for listing all modules.
2.In javascript files that defines any new angular module, use this kind of comment
 /**
  * @class angular_module.MyModule
  * @memberOf angular_module    
  */
This will add an item in the above listing of all angular_modules, as well as creating a separate html page for MyModule, because it is a class.
3.For each angularjs service, use the following comment:
 /**
  * @function myService
  * @memberOf angular_module.MyModule
  * @description This is an angularjs service.
  */
This will add an item in the MyModule page for the service. Because it is added as a function, you can write documentation for input parameters using '@param' and return values using '@return'.
4.If I have quite long codes in a controller or directive of MyModule and want to have a separate html file to document it, I will annotate the controller or directive as a class using full path. e.g.
 /**
  * @class angular_module.MyModule.MyController
  */
In this way, MyController will be listed as one item in MyModule's documentation page.
Then, we can annotate codes within the controller as member functions of MyController.
 /**
  * @name $scope.aScopeFunction
  * @function
  * @memberOf angular_module.MyModule.MyController
  * @description
  */
In this way, this function's documentation will appear in the html file of MyController's html page. The dot-separated full path string builds the connection.
There are three types of syntaxes for namepath:
- Person#say  // the instance method named "say." 
- Person.say  // the static method named "say." 
- Person~say  // the inner method named "say."
However, one imperfect point of commenting controller as a class is that a "new" will be found before the controller name in the generated html documentation because it is described as class constructor. 
- Furthermore, you can define namespaces in order to add a hierarchical structure. For example, you can define a namespace to include all controllers  - /**
 * @namespace MyApp.Controllers
 */
 
, and prefix all controller with MyApp.Controllers. You can also define namespaces like MyApp.Product or MyApp.Customer etc. 
Although not perfect, I like using jsdoc to document angularjs codes because
- It is simple;  
- The module-controller-function hierarchy are kept; 
- And it keeps jsdoc's merit that it is a browsable documentation site.
A table style jsdoc stylesheet:
Particularly, I've adapted the default jsdoc stylesheet to a table style like the Java API documentation. It looks clearer. 
In Windows, I replace this file: C:\Users\user1\AppData\Roaming\npm\node_modules\jsdoc\templates\default\static\styles with this file https://github.com/gm2008/jsdoc/blob/master/templates/default/static/styles/jsdoc-default.css
That's it.