A keyword rich, sitewide meta description is the best way to have your entire site wiped off the SERPs for dupe content, or bunged into the supplemental index.
http://www.ragepank.com/articles/43/duplicate-content/ explains how a sitewide meta description can screw you over big time.
Supplemental pages are not unique looking enough, or don't have enough links. If you have a dynamic site, it's easy to have thousands of pages that aren't particularly unique looking. If you have 1000 low-value pages, and only 50 high-value pages, google may just say "Bah, too hard" and chuck the whole lot into the supplemental index.
My advice is to block Googlebot from seeing the low value pages via robots.txt, rel=nofollow or meta noindex. This increases the signal to noise ratio on your site. Hopefully Google will remove your rubbish looking pages and add the good pages to the main index. Once this happens, see what you can do to make your rubbish pages look less rubbish, and get them indexed again.
I had a real problem with machine generated pages going supplemental, because they looked too machine generated. The solution was to add a few sentences of unique content to the top of each page, and it works. I chip away at it by fixing a couple of records per day. If you are suffering from uniqueness, nothing works like hand-written content.
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