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They are very white hat SEO and very clean. No reason to be punished!
What to do now?
Do they each have unique meta descriptions and titles?
Do you have code heavy pages from a template?
Do you use css?
Do many of your pages have small content (a para or two) but lots of code?
Do many of your pages have loads of images and little text?
Have you checked your navigation with xenu?
Supplementary results are rarely a white hat / black heart issue; they are much more likely to be a code issue
In addition to what has been listed:
From what I think I may, or may not understand from the G representatives, many pages that are in the supplemental index, are relegated there due to insufficient PR, and are not considered by G important enough to be in the main index.
I do not agree with this strategy, if this is indeed what they are doing.
Back to watching,