Remove malicious files and/or files you are not familiar with.
While many PHP applications generate files you may not be familiar with, it is important to watch for files or directories that may sound suspicious such as 'wellsfargo' or 'abbybank'.
Update all scripts/applications to the newest versions available.
Old security holes are updated and remedied in new versions of software, so updating to the newest versions available ensures that you are running the most secure option available. If you installed these applications using Simple Scripts, automatic updates are available by clicking the 'Update Now' button. For installations done with Fantastico, the main Fantastico screen will show a link on the right-hand side of the screen with the available versions you can upgrade to.
Update all plugins to the newest versions available.
Just because your applications have been updated doesn't mean the plugins you use have been also. Popular plugins for Wordpress, Joomla, Drupal, etc are created for specific application versions. When updating your applications, make sure the plugins you're using are also certified to work with the newest version of your software.
Delete any databases/applications from your account that are no longer in use.
Each databases/application you have installed on your account is another possible point of entry for attackers. By removing applications/databases that are no longer used, you will be eliminating the potential for those outdated scripts to be exploited.
Fix dangerously writeable permissions.
Most website files should be set at 644, and folders should be set to 755. This can be adjusted in an FTP client or by manually changing it in the Control Panel File Manager by selecting the file, and clicking on the icon at the top of the screen that says, 'Change Permissions'.
Hide your configuration files.
Moving your config.php and other files containing passwords to a secure directory outside of the 'public_html' folder will make them inaccessible to general web surfing.
Tweak your php.ini file.
The 'php.ini' file on your account is file that adjusts how PHP behaves on your account. By adjusting the properties of this file, you can greatly increase aspects of your security. This file is generally located in your 'public_html' directory. If you're unable to see this file, you may need to manually generate one. You can manually generate one by logging into your Control Panel and clicking the 'PHP Config' icon located in the section called 'Software/Services'. You'd then click the button that says, 'Install Master PHP.ini File'. This will install a file in your 'public_html' directory called 'php.ini.default'. To make this file active, you will then need to rename it to 'php.ini'.
Connect to your account using a secure network.
If you're connecting to the internet using a wireless connection, make sure the wireless network is using a method of security such as WPA or WEP encryption.
Make sure your local computer is secure.
One of the biggest security holes in Internet site security is accessing your site from an insecure computer. Viruses, malvare and keyloggers can be installed on your computer covertly and can be used to obtain your username/password credentials or to infect your website files themselves. Practice good at-home computer security by regularly running a reliable anti-virus/spyware scanner.