Recently I have had to deal with some insecure PHP scripts on a couple of servers that have caused us some serious problems, as well as time, to recover from.
I am going to list some of the important steps you can take to protect your server and your site from insecure PHP applications. This will by no means a complete list of items to stop them, but this should help prevent most of the basic attacks ("script kiddie" attacks - where the attacker doesn't have a great deal of skill and is depending on a preset scenario).
Most of these solutions will assume you have some level of control (root) over the server.
* Turn off allow_url_fopen: This modification will prevent the use of http://www.domain.com/somescript.php and ftp://www.domain.com/somescript.php from being used in include(), include_once(), require(), require_once(), as well as fopen(). This will prevent a hacker from including malicious code remotely. This modification will prevent the vast majority of hack attempts in PHP from working.
The downside of this modification is that some legitmate applications that use fopen() to open a remote web page might be broken. You can encourage users to use the PHP curl functions instead as they accomplish the same results.
Edit your php.ini and change allow_url_fopen = On to allow_url_fopen = Off and restart your web server.
* Use open_basedir: open_basedir allows you to dictate which paths PHP is allowed to access for a given site. Generally we set this to the path of the website (/var/www/html), /tmp (for writting session data as well as for file uploads), and the path to the PEAR repository.
The good thing about open_basedir is that it is default deny, meaning if you don't specify the path in the open_basedir it is blocked.
The bad part about open_basedir is that it come sometimes block access to legitmate applications needed by your PHP applications (Gallery is one that comes to mind, as it makes use of some external applications in /usr/bin, so you must open access to that location).
Generally, you should use this directive for every website you host as it allows you to control which directories PHP can access and you can make sure that those directories have the correct permissions to prevent potential exploitation.
* Mount /tmp noexec, nosuid and nodev: This one is particularly useful as it allows you to tell the operating system not to run any applications in a given area of the hard drive. I can tell you personally that this one as saved me numerous times. When used in combintation with the open_basedir directive you can effectively limit what the hackers have access to, and what they are able to run.
If you have a seperate /tmp partition on your hard drive you can edit the /etc/fstab file and change the options for the /tmp line.
/dev/hda3 /tmp ext3 noexec,nosuid,nodev 0 0
If you don't have a seperate /tmp partition you can create one as a loopback filesystem and mount that as noexec. I will make a seperate post on how to do this later.
* Mount your web space noexec: This might not be possible, but is a great option just like mounting /tmp in noexec. The reason for this is to prevent binary applications from being uploaded and executed in your webspace. Like I said this might not be possible, but is an excellent prevention method to prevent local root exploit binaries (where a binary exploits a problem in the kernel to gain escallated priviledges on the server, the /proc race in the 2.6 kernel is a recent example of this type of exploit).
* Make sure your permissions are correct: You should not allow world write permissions on any files, other than those required (configuration files that are written by the web server, etc). This is very important as it will save you a great deal of trouble in the event that a hacker does gain access to your site, as they won't be able to overwrite your files. Additionally, you should only allow write access to specific folders where needed.
* Prevent PHP from parsing scripts in world writtable directories: This will prevent hackers from uploading malicious scripts and running them from your site. This is a great way to tighten security, and is pretty easy to manage, just set "php_admin_flag engine off" for any directory that can be written to by the web server user. This one will save you more hassle than you can ever imagine.
* Install mod_security: Mod Security is basically a web server firewall, allowing you to block specific types of requests, as well as inspect data as it is sent to the server. My only problem with mod_security is that it isn't default deny, which means you must identify what is blocked, rather than identifying what is allowed and rejecting everything else. Still it has its uses and you should have it installed in order to react to problems that do not have patches available yet.
We hope that this list of items will help protect your server from hackers and allow you to have some peace of mind that your sites are as secure as you can make them.