Update: Disavow did not lead to a recovery. Something else happened. But I know not what! Something to do with site-wide links I think. Strange. I removed a bunch of site-wide blogroll-like links to other, highly reputable websites, and the site bounced back.
Seems that one site that I manage has made a slight recovery since filing a Google Disavow report for a bunch of directory links which were created a couple of years ago.
Get ready for some awesome MS Paint editing:
Penguin hit the site on 22nd May. On 4th June I disavowed some directory links which had keywords instead of domain name as anchor text. Partial recovery made.
Visitor Comparison
Comparing a full week after Penguin 2 with a full week before:
Visits between 26-May-2013 and 01-Jun-2013 fell by 59.35%, compared to visits from 12-May-2013 to 18-May-2013.
Comparing a full week after Disavowing links with the same pre-Penguin week:
Visits between 15-Jun-2013 and 21-Jun-2013 fell by 27.60%, compared to visits from 12-May-2013 to 18-May-2013.
Comparing the Post Disavow with the Post Penguin 2:
Visits between 15-Jun-2013 and 21-Jun-2013 increased by 78.09%, compared to visits from 26-May-2013 and 01-Jun-2013.
So, it seems that disavowing dodgy directory links may certainly assist in a Penguin recovery, although overall traffic is still down by around 28%.