I have loads of supplemental results, all of them being in sub directories I have abandoned after moving the pages, or with old urls I don't use anymore.
This whole site had about 6000 listed urls a few weeks ago, that went down to as little as 900 around christmas and now the site:
www.mydomain.com command shows just over 4000 pages again.
I introduced new sub directories and re-direct all queries from the old flat design to these new urls. This of course resulting in a massive amount of new supplemental results.
However, the new urls are doing fine, and have regained their old position in SERPs.
So don't be scared of the Supplemental results tag. It doesn't seem to hurt the rest of your site at all in my oppinion
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