There are two fantastic posts already on upgrading to OS X 10.11 El Capitan from 10.10 Yosemite regarding Apache. 

I followed the instructions and found that Apache still was giving me Internal Server errors and Internal Server error 500s. It turned out for whatever reason; the mystery was my vhosts needed error logs.

Previously my vhost entries looked like this:

<VirtualHost *:80>
       DocumentRoot "/Users/emerge/Development/site/"
       ServerName site.lvh.me
        <Directory  "/Users/emerge/Development/site">
                AllowOverride All
                Require all granted
        </Directory>

</VirtualHost>

Once I added both the error log and custom log, I stopped getting the errors.

<VirtualHost *:80>
      DocumentRoot "/Users/emerge/Development/site/"
      ServerName site.lvh.me
      ErrorLog "/private/var/log/apache2/site-error_log"
      CustomLog "/private/var/log/apache2/site-access_log" common
       <Directory  "/Users/emerge/Development/klarquist/_html-cuts">
               AllowOverride All
               Require all granted
       </Directory>

</VirtualHost>