For this you have to override preprocess region
function MYTHEME_preprocess_region(&$variables) {
if(CONDITION){
$variables['theme_hook_suggestions'][] = 'regionspecial__' . $variables['region'];
}
print_r($variables['theme_hook_suggestions']); // comment this statement
}
After that your template suggestion name will be 'regionspecial--content.tpl.php' For certain desired condition. Once you clear Drupal's caches your new template file should start being used for that region. It might be worth noting that you'll probably need a copy of the core region.tpl.php file somewhere in your theme folder as well, or the theme registry might not pick up your custom file.