I had many pages from some sites being marked as supplemental at google. I tried many things but what worked for me was this: I changed the URLs. Originally, I use rewrite rules to redirect x1.html to index.php?p=x&id=1. After going supplemental, I changed the URLs to be x-1.html instead of x1.html (and still redirects to the same index.php?p=x&id=1). Also, I added a 404 not found header to all the x1.html type files (in some sites, I used a redirect header instead of 404). In few weeks only, the site got re-spidered and the new URLs are not supplemental anymore. Hope this helps anyone.