Forum Moderators: Robert Charlton & goodroi
Study of these threads will pay dividends:
Supplemental Results [webmasterworld.com] - what exactly are they?
Duplicate Content [webmasterworld.com] - get it right or perish
Duplicate Content [webmasterworld.com] - comments from Google's Adam Lasnik
Google PR [webmasterworld.com] - Page Rank FAQs
One reason for a non-duplicate pdf file to get a Supplemental tag could be low PR. How many links are likely to point to the average PDF file? It's not usually on a site-wide menu or even in the sub-section menu. So unless it offers some real powerhouse information, linked to directly by other sites around the web, a PDF file is often tagged Supplemental. If the pages that do link to the pdf gain in PR strength, then so does the pdf file.
By the way, the threads I linked to above are also linked from the Hot Topics [webmasterworld.com] area, which is always pinned to the top of the Google Search forum's index page.
Some pages just don't belong in the results for frequently searched terms - see the "comments from Adam Lasnik" link above for his remarks. And for a very precise search, even a url with a Supplemental Result tag can still show up in the top ten.