We don't have a Sphinx style guide ... so I guess it's a matter of taste and what you want to convey to the user.

With ```:meth:`~iris.cube.Cube.change_units` ``` Sphinx renders the link as ```change_units```

If you want the class namespace context to help the user then ```:meth:`iris.cube.Cube.change_units` ``` without the ```~``` renders the link as ```iris.cube.Cube.change_units```.

The other approach ```:meth:`Cube.change_units <iris.cube.Cube.change_units>` ``` allows you to associate any text with the link, which is a tad dangerous in my opinion as you might change the class method name but not change the text. So you could end up with ```:meth:`Cube.change_units <iris.cube.Cube.wibble>` ```.

If in doubt I'd default for the full namespace option i.e. without the ```~```.