I agree, but I've thought of everything I can think of, I have no idea what the problem might be at this point.
1. Off-theme reciprocal linking; Never did off topic linking
2. (Excessive) linking between sites on the same IP ... haven't done this either
3. Unnatural link growth (lots of links in a short space of time); nope
4. Unnatural link loss (a link network drops you);
don't think this is it
5. Duplicate content: 20000 pages with little unique content in each;
I did have some datafeeds on a couple of sites - but I took those down months ago. Not nearly as many as 20000 though
6. Another site doing 302 redirects to yours;
this I don't know, and wouldn't know what to do about it if it was happening.
7. Another site copying your content.
could be, but I wouldn't know how to stop it either
8. (Possibly) 8000 low PR links, and very few decent, authority sites linking to you (unnatural).
I've got an ODP link
9. The addition of 1000's of pages suddenly;
no, all pages are hand written
10. Linking to bad neighbourhoods;
I took down any suspicious looking links a while back on one site
11. Lots of affiliate links (use rel="nofollow" in these)
11a. Using a redirect script for your own links.
I had quite a few with the affiliate links, but again those were taken down a long time ago. I don't think the affiliate links that are left would be a problem
12. Running a directory, especially with entries drawn from DMOZ or other SE results.
Plus the usual grey SEO tricks done to excess: e.g. excessive use of <H1> tags modified by changing the font size so it's not actually H1 size, that sort of thing.
I use one H1 per page - according to proper html standards, and I keep them reasonably big. Although interestingly I heard someone else mention css being a problem with this update.
In other words:
'Authority' sites that get links from other quality sites, from diverse sources, will triumph over tricksy, 'me-too' upstarts every time, in the long run.
How do you naturally attract links to your good content if no one can find your site in the serps to know it exists to be able to link to it? That is a big problem I've had.
some others to add:
13) too many link exchanges of any type - I stopped doing these a year or so ago - I don't think what is left could do that much harm
14)paid links or those that look like them - I've never had the money to buy paid links. Do I have links that look like they may have been paid for? I don't know, since I don't know what SE's think a paid link looks like.