I've spent several almost sleepless nights now, completely overhauling all the websites I have. I've cleaned them up, upgraded the HTML, rewritten PHP, added all sorts of things for SEO, and finally I am fairly happy. I have deleted some, I have resurrected some. I still have a couple of small packages to upgrade - Serendipity and SquirrelMail - and one very old website to completely rewrite to PHP. But finally I have a grip on it all.
Probably by the end of the year, I hope to see Google's disapproval of me lifted.