sites-available contains the apache config files for each of your sites. For example:
<VirtualHost *:80>
ServerName site.mysite.com
ServerAdmin my@email.com
DirectoryIndex index.php
DocumentRoot /home/user/public_html/site.mysite.com/public
LogLevel warn
ErrorLog /home/user/public_html/site.mysite.com/logs/error.log
CustomLog /home/user/public_html/site.mysite.com/logs/access.log combined
</VirtualHost>
When you want to add a new site (for example, site.mysite.com), you add it here, and use:
a2ensite site.mysite.com
To enable the site. Once the site is enabled, a symlink to the config file is placed in the sites-enabled directory, indicating that the site is enabled.