function w($cont, $filename) {
    if (is_writable($filename)) {
        if (!$handle = fopen($filename, 'a')) {
            echo "不能打开文件 $filename";
            exit;
        }
        if (fwrite($handle, $cont) === FALSE) {
            echo "不能写入到文件 $filename";
            exit;
        }
        echo "成功地将 $somecontent 写入到文件$filename";
        fclose($handle);
    } else {
        echo "文件 $filename 不可写";
    }
}
$cont_a = file_get_contents("/path/filenameA");
$arrA = explode("\n", $cont_a);
$cont_b = file_get_contents("/path/filenameB");
$arrB = explode("\n", $cont_b);

$arrNewB = array_diff($arrB, $arrA);
$cont_newb = implode("\n", $arrNewB);
$arrC = array_diff($arrA, $arrB);
$cont_c = implode("\n", $arrC);

w($cont_newb);
w($cont_c);

------解决方案--------------------

貌似array_diff函数 + file函数就行了，LZ试下效率如何。