Most of the forums have some discussion of supplemental issues going on at any given time. Lots of people seem confused by what it means and what they can do about it.
Here’s my take on it:
A page in the supplemental index hasn’t got a penalty, it hasn’t been ‘filtered’, its just that Google doesn’t think its very important. This may not be very complimentary for your dearly beloved site, but Google has millions (Billions? Trillions???) of pages. They have to prioritise them somehow.
Here’s my ‘3 points to examine’ to try to get pages out of supplemental hell:
* Does Google recognise the page as special and unique? (Is the title unique? Is the meta description unique? Each page should have unique titles and descriptions – and that’s easy because each of your pages is distinct and is about one specific topic, right?)
* Does Google believe that the rest of the internet knows about my page (You have external deeplinks to as many pages as possible, right?)
* Can Google easily find these inner pages? (If Google is barely aware of a page why would they put it in the Important index?)

Lets talk about the third point above a little more, because I haven’t seen it discussed in relation to the supplemental index before.
I think Google may mark a page as supplemental when it can’t easily reach it – the old ‘3 clicks from the homepage’ rule. This happens because if the page is hard to get to then it can’t be important, can it? Doesn’t seem unreasonable.
So, what can you do? Make sure your site has strong crossflow – by which I mean (yes, I just made ‘crossflow’ up ;)) that each page must have links from several other pages to it – you must be able to move around your site easily.
For example:
– your homepage should link to several deep pages
– you should have a html sitemap that includes all your pages (if you have a ridiculous number of pages – say more 1000 then have multiple sitemaps). Link to your sitemap.html from every single page, just like you link to your home page from every page.
– from each deep page, link to as many other deep pages as is sensible. Lets call these sibling links.
– if it makes sense to have category summary pages then have them, and make sure all the pages that the category summary page points to, point back to that category summary page. Lets call them parent links.
The idea is to make movement around your site as easy as possible.

Does this work for me?
Yes – I have sites with 3000 pages and I have approx. 10 pages in supplemental. I assume that Google has just not gotten to a complete crawl for those last few, despite sitemaps and pings and every other means I have to tell them.

Give the site good crossflow and fewer pages will be in supplemental.