PHP Fatal error: Allowed memory size of on indexer.php action

The problem comes from .htaccess. One of the values is php_value memory_limit 256M. This doesn't make sense on the first view, but on the second it is explainable.

I don't know why magento implemented this idiot thing, but what happend is, the following method reads the information from .htaccess and processes them:

\Mage_Shell_Abstract::_applyPhpVariables
protected function _applyPhpVariables()
{
    $htaccess = $this->_getRootPath() . '.htaccess';
    if (file_exists($htaccess)) {
        // parse htaccess file
        $data = file_get_contents($htaccess);
        $matches = array();
        preg_match_all('#^\s+?php_value\s+([a-z_]+)\s+(.+)$#siUm', $data, $matches, PREG_SET_ORDER);
        if ($matches) {
            foreach ($matches as $match) {
                @ini_set($match[1], str_replace("\r", '', $match[2]));
            }
        }
        preg_match_all('#^\s+?php_flag\s+([a-z_]+)\s+(.+)$#siUm', $data, $matches, PREG_SET_ORDER);
        if ($matches) {
            foreach ($matches as $match) {
                @ini_set($match[1], str_replace("\r", '', $match[2]));
            }
        }
    }
}