I think the supplemental index still exists, it just isn't the supplemental index anymore. From the somewhat cryptic posts I have seen, the way pages go into this other index, and they way that queries are processed through the index have changed drastically since it was called the supplemental index. I do see a lot of pages indicated as being not in the main index, but these same pages are frequently at the top of other types of searches. For example, if you do a search in Google's blog search for Matt Cutts blog (chosen because it gets so many links) most of the top results are (or were as of last week) in this other index. Granted, that could be because his blog has some serious duplicate content issues...

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The best way to learn anything, is to question everything.