If you have a class defined within another class, its definition is ignored, and any methods and properties of the nested class are documented along with the documentation for the outer class.
SfApexDoc supports this, and displays the nested classes info below the main classes info. (it has a bug and it shows all the way below the menu list).
If you have a class defined within another class, its definition is ignored, and any methods and properties of the nested class are documented along with the documentation for the outer class.