Some of you may have encountered a malware warning when on the website. Please do not be alarmed.
Earlier this year our site became infected with two separate programs. Both have been removed. The first was more of an annoyance: it just generated error messages until the log files used up all of our free space, causing the site to crash. The second was a little more insidious: it looked for Internet Explorer users who played a certain online game (I don't remember which one) and then locked all the user's points and tried to ransom them.
Both items were removed and the site was rebuilt on an entirely different server.
Each of the malicious programs had a distinct signature. I have embedded those signatures in a program that I run regularly. The code is not executed; I search every file on our system for code containing these fragments. It is that code which causes the malware warning.
In addition to traditional anti-virus software and the additional custom scan that I run, I receive a notification of every file on the system that gets added or modified.