With new Ubuntu 13.10 Apache has new naming scheme for sites configuration files. Because of this your virtual servers might stop working, showing default site, which is “It works!” page, or whatever you have configured for your web server.
To fix the problem, you have to delete all old links in /etc/apache2/sites-enabled (maybe keeping 000-default.conf if you like), rename all site configuration files, residing in /etc/apache2/sites-available, to have .conf postfix, and then enable it again by manually creating a symbolic link to sites-enabled, or using a2ensite tool.
You can also use this simple shell script:
for i in `ls -1 /etc/apache2/sites-available | grep -v -e '.dpkg' -e '.conf$'` do rm /etc/apache2/sites-enabled/$i mv /etc/apache2/sites-available/$i /etc/apache2/sites-available/$i.conf a2ensite $i done
That should do the trick. Note that a2ensite accepts only the site name, without .conf postfix.