Search engines researchers use two main concepts to identify the success of search engine algorithms: precision and recall.
Precision measures how accurate the algorithm is in finding the best matches for our searches. Recall measures how comprehensive the algorithm is in finding as many relevant results as possible.
In their effort to fight spam Google has filtered out a lot of pages that would otherwise rank. They have created a separate index for such pages which they call the supplemental index.
Basically this is an effort to improve the comprehensiveness of the search engine — the recall. If there are no pages in the main index for a particular search, they will at least have the supplemental results.