Clicking any administration menu link results in empty overlay screen
The issue turned out to be caused by me including jQuery via the following line in my theme's info file:

scripts[] = js/jquery-3.1.1.min.js


Removing this line and using the jQuery version included by default (1.4.4) will return the $ is not a function error when using $() syntax, which can be resolved by wrapping existing jQuery code in the following:

jQuery(function ($) {
  // ...
});