Estimate shipping on the shopping cart page lists all countries in the country drop-down. It should only list those countries where shipping is enabled in Admin -> Configuration -> Shipping
One caveat though... Not all shipping plugins use "Shipping Method Restrictions". (I think only the core By Weight does. Also a couple of 3rd party, like By Total). And with multipl "methods", which to look at? (All?)
Currently, if you're limiting your registration & shipping & billing addresses you could just remove the unwanted countries from the Country table.
BTW, on the "Shipping Method Restrictions" page, the check box on top of each column toggles all ON, but does not work to toggle all OFF.