The Supplemental Index of Google has been a hotly discussed topic in the past, see Expert Comments On Supplementary Index. Some people had also come up with SEO tools for assessing it. See: Google Supplemental Index Ratio Calculator: New SEO Tool!
What's the purpose of the Supplemental Index? Google's Official Webmaster Blog says that "it stored unusual documents that we would search in more depth for harder or more esoteric queries."
Further, "For a long time, the alternative was to simply not show those documents at all, but this was always unsatisfyingĂ˘â‚¬â€ťideally, we would search all of the documents all of the time, to give users the experience they expect."
Consequently, they say that after having done away with the "supplemental index tag,Ă˘â‚¬Âť they are now Ă˘â‚¬Ĺ“…coming to the next major milestone in the elimination of the artificial difference between indices: rather than searching some part of our index in more depth for obscure queries, we're now searching the whole index for every query."
So from now on even a normal query would return results from all indices including the "Supplemental Index." So how does this help the user after all?
They say that "From a user perspective, this means that you'll be seeing more relevant documents and a much deeper slice of the web, especially for non-English queries." and for webmasters "this means that good-quality pages that were less visible in our index are more likely to come up for queries."
However, there are still questions about it in people's minds, as can be seen from discussions at various forums. At webmasterworld tedster comments "Supplemental urls only received a partial indexing in the past – just the top level elements were searchable, like the title and meta description….the 'deep' body content on a supplemental url was not truly indexed in a searchable manner." There's no clarification about the issue from Google's blog post.
Some want the Supplemental Index to stay, one webmaster says "Not knowing which pages are in the supplemental index hurts webmasters trying to improve the quality of their site. PLEASE!!!!! Leave the supplemental tag on the results so we have a chance of improving our web sites content."