Custom scales are not respected by matplotlib 1.2.0, as can be seen comparing the two gallery examples
http://matplotlib.org/1.1.1/examples/api/custom_scale_example.html
and
http://matplotlib.org/examples/api/custom_scale_example.html

A quick print of matplotlib.scale.get_scale_names() shows that it is in the list. However, it does not seem to be applied when calling gca().set_yscale('mercator'). Calling gca().set_yscale('log') works however.