How to override system_time_zones in Drupal 7
I was able to access the timezone dropdown list by implementing hook_form_alter() with an #after_build function.  You can filter, clean and modify the array here.

function MYMODULE_form_user_profile_form_alter(&amp;$form, &amp;$form_state) {
   $form['#after_build'][] = 'MYMODULE_timezone_modify';
}

function MYMODULE_timezone_modify($form, &amp;$form_state) {
   $form['timezone']['timezone']['#options'] = array(/*Your New or Modified Array Here*/);
   return $form;
}