I recently updated one of my development machines to Ubuntu 13.10 which now uses Apache 2.4 by default. In my case, I had updated a machine that was previously running Ubuntu version 13.04 and had been running Apache 2.2.
After the upgrade, I was disturbed to find that none of my sites worked! I kept getting Apache 403 (Forbidden) error messages. I figured the upgrade had changed my configurations or something... but after fruitlessly messing with the config files (and seeing nothing wrong with them) I figured I'd look in the apache error log, which is located in /var/log/apache2/error.log by default on Ubuntu 13.10. To my surprise, I found lots of the following errors:
AH01630: client denied by server configuration: /path/to/my/sites
I had never seen that before. Then I noticed at the top of the log file "AH00163: Apache/2.4.6 (Ubuntu)". Ohhhhh.... So we're using the new 2.4 eh? After some google searches, I found out that Apache 2.4 comes with some security enhancements that attempt to make it more difficult for hackers to hide their files on a compromised system. That's neat, but I need to get my sites to work.
After reading a bit of the 2.4 Access Control Documentation, I found that a quick easy fix is to add a directory rule to your main apache config file (/etc/apache2/apache2.conf by default on Ubuntu):
<Directory /path/to/my/sites> Options Indexes FollowSymLinks AllowOverride None Require all granted </Directory>
Restart Apache, and boom, all sites are now loading just fine. The idea behind these rules is to make it so that hackers who, say, use SQL injection to access your PHP site, have a harder time hiding their files in obscure directories on your system, amond other things.
Hope this helps!