I had a site, which was penalized for over a year.
I now believe that it was probably because it had a previous owner who did something evil with it but I was not aware of that. It was simply an expired domain with no PR, no backlinks, no directory listing, and no record of a previous existence in TIA.
The site was crawled every day and had hundreds of backlinks but Google showed none of them and the site was PR 0/10. The only way to make the site show in a SERP was to search for the domain name.
I wrote to email@example.com repeatedly asking why the site was banned or penalized.
They wrote back repeatedly and said, "we don't do that."
I wrote back with proof.
They wrote back and said that I was wrong and that they don't do that.
I wrote back with more proof.
This went on for 14 months.
One day the entire site just appeared in the SERPs, as if by magic.
With some sites, only time will fix such problems, with others, nothing ever will.