There is not much I can tell about your particular scenario, however, I can say this.
Google does check black lists and Google does get nervous if your site disappears for a period. Check http://mxtoolbox.com/blacklists.aspx to see if your domain name and/or IP address is blacklisted anywhere. Remove from any blacklists the best you can and wait.
Fortunately, Google is rather forgiving. Some blacklists are not much of a concern to Google but an indication of something wrong.
Still it will take a quite a while for your domain name to rebuild trust. Time and consistency are the only cures. Once Google sees that the issues are over, your trust score will begin to rise again and your placement in the SERPs should return. But you will have to be very patient. It will pay off in the end.