Here is my configuration / notes about securing a php installation.

These configuration rules are taken from the .htaccess file configuration of Joomla, and I've adapted it for apache. They address some common exploits.

<IfModule mod_rewrite.c>
    RewriteEngine On
    
    ## Begin - Rewrite rules to block out some common exploits.
    # If you experience problems on your site block out the operations listed be
    # This attempts to block the most common type of exploit `attempts` to Jooml
    #
    # Block out any script trying to base64_encode data within the URL.
    RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
    # Block out any script that includes a <script> tag in URL.
    RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
    # Block out any script trying to set a PHP GLOBALS variable via URL.
    RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
    # Block out any script trying to modify a _REQUEST variable via URL.
    RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
    # Return 403 Forbidden header and show the content of the root homepage
    RewriteRule .* index.php [F]
    #
    ## End - Rewrite rules to block out some common exploits.


    ## Begin - Joomla! core SEF Section.
    #
    RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
    #
    # If the requested path and file is not /index.php and the request
    # has not already been internally rewritten to the index.php script
    RewriteCond %{REQUEST_URI} !^/index\.php
    # and the request is for something within the component folder,
    # or for the site root, or for an extensionless URL, or the
    # requested URL ends with one of the listed extensions
    RewriteCond %{REQUEST_URI} /component/|(/[^.]*|\.(php|html?|feed|pdf|vcf|raw
    # and the requested path and file doesn't directly match a physical file
    RewriteCond %{REQUEST_FILENAME} !-f
    # and the requested path and file doesn't directly match a physical folder
    RewriteCond %{REQUEST_FILENAME} !-d
    # internally rewrite the request to the index.php script
    # RewriteRule .* index.php [L]
    #
    ## End - Joomla! core SEF Section.




</IfModule>

Not all the directories of your website are the same; some of them must allow the execution of php, some others not. In the case you have to allow php execution, you have use “php_admin_flag engine On” to allow php execution in that directory:

<Directory "/var/www/YOUR-DIRECTORY/">

    Options -Indexes +FollowSymLinks

    AllowOverride None

    php_admin_flag engine On

    php_admin_value open_basedir "LIST-OF-DIRECTORIES-HERE"
    php_admin_value include_path "ALLOWED-INCLUDE-DIRECTORIES-HERE"    
    php_admin_value upload_tmp_dir "ALLOWED-TMP-FILES-HERE"
    # you can configure any php param here: 
    php_admin_value post_max_size "25M"
    php_admin_value upload_max_filesize "20M"
</Directory>

PHP execution must be restricted in those directories where it's clear won't be any php file in them:

<Directory "/var/www/MY-WEBSITE/UPLOADED-FILES">
    # To avoid c99.php injection
    php_admin_flag engine Off
</Directory>

For instance, you can restrict the access to your logs directory of your website at all to avoid someone could guess the url and try to gain access to the logs content:

<Directory “/var/www/MY-WEBSITE/logs”>

  <RequireAll>
      Require all denied
  </RequireAll>
  php_admin_flag engine Off

</Directory>

Imagine you have a directory of php files you only want through a cron file: in that case, specify that those directory cannot be reached from any place, but from inside of the machine only:

<Directory "/var/www/MY-WEBSITE/RUNNING-FROM-INSIDE">
            <RequireAll>
                    Require local
            </RequireAll>
</Directory>

In the apache configuration of the virtual host, open_basedir must be configured and must point to the directory of the web application or deeper, to ban php to open other files that aren't in the installation.

Example:

    <Directory "/mywebsite">
        php_admin_value open_basedir "/mywebsite:/dev/urandom"
    </Directory>

include_path is another funny thing. It specifies what php files can be read by the include command: it's better to specify the more constrained directory possible: if the application has an “include” directory, specify this directory only, to avoid an attacker to read configuration files or other information.

This configuration must be set per virtual host, and it's better to set a non-existent file in the main php.ini file.

Example:

  php_admin_value include_path "/mywebsite/include/"

This is a frequent source of problems. And I misunderstood that many times, until somebody kindly let me know about this, by injecting c99.php in my website. This directive configures the directory where upload files must be placed when loaded: it's a very bad idea to have them inside your website, because it allows an attacker to upload any php file and execute it afterwards.

Example:

php_admin_value upload_tmp_dir "/tmp"

Configure engine on only if you need php in the virtual host:

Example:

php_admin_value engine On

In any other website, turn it off.