Our site was placed under a manual penalty last year in June 2012 after penguin rolled out. We were advised by Google that we had unnatural links pointing to our site. We fought for months, running backlink checks and contacting webmasters where Google's WMT was showing the sites which had links. We have submitted numerous reconsideration requests with proof of our efforts in the form of huge well labeled spreadsheets, emails, and screen shots of online forms requesting link removal.
When the disavow tool came out we thought it was a godsend and added all the sites who had either ignored us or refused to take down the links to the disavow.txt with the domain: tag. Then we submitted another reconsideration request, but to no avail.
We have since had email correspondence with a member of the Google Quality Search Team who after reviewing the evidence of all our previous reconsideration requests and disavow.txt still advised us to make a genuine effort and listed sites which had inorganic links pointing to our site which were already included in the disavow.txt.
Google has stated "In order for your site to have a successful reconsideration request, we will need to see a substantial, good-faith effort to remove the links, and this effort should result in a significant decrease in the number of bad links that we see."
We have truly done everything we can and proven it too! Especially with all the sites in the disavow.txt there must be a decrease in links pointing to our site. What more can we do?