If you need to make a static backup of a dynamic site you are going to find that you can't access the pages because apache is trying to parse the URL string.
You will have something that looks like "index.php?module=". and it needs to look like "index.php%3fmodule="
perl -pi -e 's/index.php\?/index.php\%3f/g' ./*
Will change all of your links so you can access the backup.