Is there a good way to set available countries in Drupal Commerce shipping and billing?
Depends what you mean by 'quick', really. Yes, you can do it programatically. With PHP:

$instance_config = field_info_instance('commerce_customer_profile', 'commerce_customer_address', 'shipping');

$instance_config['widget']['settings']['available_countries'] = array(
  'GB',
  'US',
  'FR',
  // etc...
);

field_update_instance($instance_config);


Or with JS (I'll let you work that one out, selecting a bunch of &lt;option&gt; tags based on a bunch of values is very easy).

IMO the time-consuming part is building up the array of default countries in the first place; no matter what automated method you use to put the values in, someone needs to spend the time choosing and preparing them. You can't get away from that.