I encountered an extremely difficult problem on my site recently when I made a fundamental mistake of uploading an image which I had not properly checked with anti-virus.
This led to my site being black listed by Google. The solution was two fold,
1. I had to return to an earlier backup of my site before the virus infected it. (In fact I actually redesigned the site from scratch, I had been waiting for a moment to do this anyway)
2. I had to access Google Webmaster Tools and appeal the black-listing
It has taken me a whole month but my site is now back up and running. The solution in future is to make sure that content is never uploaded which does not have a confirmed source and NEVER if it has not been checked by a proficient anti-virus. Now I just need to finish the re-design of the website, hopefully should be complete by next week.