I also saw this message, and it as very realistic.
The clues that told me it was fake:
* The message was a Safari window, not a "Apple Security Center" app.
* The numbers of affected files kept blinking to get my attention. Apple doesn't usually do that sort of thing.
I closed that window immediately.
I have a question for anybody who might know...
* The Safari window with the "Apple Security Center" warning listed the number of infected files on my hard drive -- and it displayed the top level of my finder window! Does this mean that my computer has already been infected in some way? Or is it normal behavior for a web site to be able to discover anything about the contents of my hard drive?