The Google Supplemental Index

This is not strictly a penalty in and of itself, but it may be the result of one. Google stores its crawled search data in two indexes: the primary index and the supplemental index. The supplemental index stores pages that are less important to Google for whatever reason. Results from the supplemental index typically appear at the end of the results for a Google query (unless the query is very specific), and the results are marked as supplemental results.
Factors that lead to inclusion of the links in the supplemental index rather than the primary index are the lack of significant unique content or a lack of inbound to the said content. It may also be as a result of explicit penalization.