The official Webmaster blog has a helpful post has a list of Quick security checklist for webmasters.
"Check your server configuration. Apache has some security configuration tips on their site and Microsoft has some tech center resources for IIS on theirs. Some of these tips include information on directory permissions, server side includes, authentication and encryption.
Stay up-to-date with the latest software updates and patches. A common pitfall for many webmasters is to install a forum or blog on their website and then forget about it. Much like taking your car in for a tune-up, it's important to make sure you have all the latest updates for any software program you have installed. Need some tips? Blogger Mark Blair has a few good ones, including making a list of all the software and plug-ins used for your website and keeping track of the version numbers and updates. He also suggests taking advantage of any feeds their websites may provide.
Regularly keep an eye on your log files. Making this a habit has many great benefits, one of which is added security. You might be surprised with what you find.
Check your site for common vulnerabilities. Avoid having directories with open permissions. This is almost like leaving the front door to your home wide open, with a door mat that reads "Come on in and help yourself!" Also check for any XSS (cross-site scripting) and SQL injection vulnerabilities. Finally, choose good passwords. The Gmail support center has some good guidelines to follow, which can be helpful for choosing passwords in general.
Be wary of third-party content providers. If you're considering installing an application provided by a third party, such as a widget, counter, ad network, or webstat service, be sure to exercise due diligence. While there are lots of great third-party content on the web, it's also possible for providers to use these applications to push exploits, such as dangerous scripts, towards your visitors. Make sure the application is created by a reputable source. Do they have a legitimate website with support and contact information? Have other webmasters used the service?
Try a Google site: search to see what's indexed. This may seem a bit obvious, but it's commonly overlooked. It's always a good idea to do a sanity check and make sure things look normal. If you're not already familiar with the site: search operator, it's a way for you to restrict your search to a specific site. For example, the search site:googleblog.blogspot.com will only return results from the Official Google Blog.
Use Google's Webmaster Tools. They're free, and include all kinds of good stuff like a site status wizard and tools for managing how Googlebot crawls your site.
Another nice feature is that if Google believes your site has been hacked to host malware, our webmaster console will show more detailed information, such as a sample of harmful URLs. Once you think the malware is removed, you then can request a reevaluation through Webmaster Tools.
Use secure protocols. SSH and SFTP should be used for data transfer, rather than plain text protocols such as telnet or FTP. SSH and SFTP use encryption and are much safer. For this and many other useful tips, check out StopBadware.org's Tips for Cleaning and Securing Your Website.
Read the Google Online Security Blog. Here's some great content about online security and safety with pointers to lots of useful resources. It's a good one to add to your Google Reader feeds.
Contact your hosting company for support. Most hosting companies have helpful and responsive support groups. If you think something may be wrong, or you simply want to make sure you're in the know, visit their website or give 'em a call√Ę‚ā¨¬Ě.
If you have more feedback or suggests visit Webmaster help.