I have just upgraded the Ubuntu Server version from 12.04 LTS to 14.04 LTS.

Indeed, as said above, the .conf extension to Apache 2.4.x is needed to the websites vhost files that resides on sites-available directory.

Before read this question I did not have a clue what was going on with the server.

Pretty nice solution.

Just summarizing I did the following steps on Terminal:

1) Access sites-enabled folder

$ cd /etc/apache2/sites-enabled

2) Because the command a2dissite will not work with deprecated files (without .conf) remove the old website files that was published

$ sudo rm <my-old-website-without-.conf>

3) Rename the website vhost files changing its extension adding .conf to the end

$ sudo mv /etc/apache2/sites-available/mywebsite /etc/apache2/sites-available/mywebsite.conf

4) Republish the new and correct vhost file

$ sudo a2ensite mywebsite.conf

5) Check the website on browser and have fun! 🙂