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I've had two clients who came to me malware warnings on their Google results. In both cases, the site owner had not done anything malicious, but yes - their server had been compromised without them knowing it.
The thing to do is to look at your source code - and follow Google's information on how to get the warning removed from the SERPs when you are sure it's fixed. The most common situation is called an "iframe injection" - so look for any code that shouldn't be there, with extra attention for iframes that you didn't put there.
This kind of parasite hosting is reaching epidemic proportions in recent times - and it's often used to form a wide base of drone computers. The iframes install trojans on the end user machines for various nefarious goals, such as DDOS attacks on major websites.
[edited by: tedster at 5:36 pm (utc) on Oct. 25, 2007]
This kind of parasite hosting is reaching epidemic proportions in recent times
Getting an entire new site indexed can be a bear of a job - although the 404's will be your friend. I'd say be sure to have a Webmaster Tools account set up first, for an authenticated communication line to Google. And since your organic traffic is minimal, it does sound like a good time to take some calculated steps.
Midsummer I was using the preview tool and one of the ads did a redirect and started a download on me. I killed the ad, put it in the filter and quickly emailed Google about it. Some time later I was checking my site out because I had begun sliding in the serps and found that page had the dire warning on it.
Again I went to Google (email) and complained bitterly about what they had done to me because of a dodgy ad that they had left go live.
Anyway it was absent for awhile until this morning when I saw the same thing again. Went to tools, did a re-inclusion with a long email in the message part of it.
Checked around and about an hour later searched for it as a stand alone and low and behold it is clean!
I suspect it was all along and this last time was from an old cache. WHY don't they clean these things out/ Others may also see the 'old' serps and there I go again fending off emails that purport to tell me off for spreading that junk.