You’re developing a Magento importer and you want to clean your DB after some tests? Here you have:

require_once dirname(__FILE__) . '/app/Mage.php';
Mage::app()->setCurrentStore(Mage::getModel('core/store')->load(Mage_Core_Model_App::ADMIN_STORE_ID));

$resource = Mage::getSingleton('core/resource');
$db_read = $resource->getConnection('core_read');

$categories = $db_read->fetchCol("SELECT entity_id FROM " . $resource->getTableName("catalog_category_entity") . " WHERE entity_id>1 ORDER BY entity_id DESC");
foreach ($categories as $category_id) {
	try {
		Mage::getModel("catalog/category")->load($category_id)->delete();
	} catch (Exception $e) {
		echo $e->getMessage() . "\n";
	}
}