It depends on the source of the warning. StopBadWare.org is a group that works with Google, and others are working to detect sites that host malware. There are three ways sites get malware on them.

* Compromised webservers can insert malicious code into all HTML pages served

* Pages which allow user-contributed HTML, where the HTML hasn't been properly sanitized

* The use of questionable advertising content, or compromised ad servers

Google published an interesting white paper. http://www.usenix.org/events/hotbots07/tech/full_papers/provos/provos.pdf
Source(s):
http://www.usenix.org/events/hotbots07/tech/full_papers/provos/provos.pdf
http://www.codinghorror.com/blog/archives/000859.html

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A lot of websites also post this to make people think they have a virus, and if you click it usually leads you to a fake anti-virus crawling with viruses.
Source(s):
Fooled my mom a million times. I'm sick of fixing her computer.

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