A painful read and it mirrors my situation with Google. I used to get good organic traffic from Google having done no SEO – just, you know, having a site that people liked. Then Google updated something and 80% of my traffic slid away.
What's distressing is that there's no point of contact, human or otherwise, that could shed light on what the issue is. Some sites get warnings in Google's Webmaster Tools, but I never have.
I've spent countless hours reading forums and implementing suggestions and as Haughey says, it's as though Google flipped a switch somewhere and there's a permanent penalty applied. Nothing I've done has had any effect.
The irony of this is that in their efforts to kill spam, Google has put sites who have never touched SEO in the position of urgently needing SEO. Or buying AdWords. Of course, Google would never be so unethical as to sabotage a site's traffic to force them to buy AdWords, which is their primary source of revenue.
Anyway, best of luck to MetaFilter. I suppose I should contact them to have links to my site removed. Sigh.