Thank you for your thoughts.
I agree that they must be swamped and most of the 'complaints' you can see on the Google forums fully deserve to be penalised in my humble opinion, but I think that the total lack of communication is more damaging than helpful.
If they want to improve the web, why do they not give more details about what is causing the problem? By being more transparent and helping webmasters to eradicate spammy techniques, everyone will be forced into improving their sites for all the right reasons.
If they don't have the resource to handle the reinclusion requests, then they shouldn't have it as an option.
I still feel that it is very poor not to even look at the files that were prepared - that shows a lack of respect.
I agree that it is likely to be something simple. The 'spike' theory is still the strongest contender for me, due to the timings of events, but that is alarming if it proves to be true as we were effectively penalised for doing exactly what Google encourages (creating good content that will naturally attract links).
Another possible cause is the fact that we have got a number of directory links over the years. Whilst I have never considered these to be high quality links, I have never seen Google saying that you shouldn't submit your site to them (indeed, they used to actively suggest that submitting to Yahoo! was a good idea) and it is a way for Google to outsource some human assessment of sites (assuming that the directories do check your sites).
If it is the directories, then the door for negative SEO is so wide open that it is alarming. As many have said, completely ignoring such links would be better than penalising you.
We are still no closer to understanding what we have done wrong, despite every effort to adhere to the guidelines and a lot of work trying to audit / document our link profile. With very little faith in the reinclusion process, where can we possibly turn to now?
We will see. There were multiple views of the open letter from Google, so somebody somewhere has seen it and I just hope that there is some form of response.
The irony is that we spend most of our life defending Google and encouraging clients to improve what they are doing online. On this occasion, I really find it hard to defend them. I appreciate that we are a drop in a mighty ocean, but the principle is one that I think is an important one and one that I will pursue.
Thanks again for your contribution,
Joe