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Before I gave up on the concept of PDF-on-6" screen, I would eke out a little more usability by cropping the headers/footers. When that wasn't enough, viewing in landscape worked pretty well. Of course you can author PDFs that are perfectly usable on Kindle by setting the page size appropriately, but that's rarely what you are dealing with in 3rd party content.
Another problem is that Kindle does not let you navigate PDF bookmarks (typically marking the beginning of chapters, etc.), or PDF links to footnotes or illustrations.
For full page PDF viewing, my conclusion is you really need at least 1024x768 resolution. Kindle DX is adequate, but again does not have navigation features that you'd expect. Performance is lacking also.
Sony Reader has always had the best small-screen PDF support. But again, there's no substitute for resolution.
PDF reflow should be seen as a last resort. In practice, for the type of PDFs I want to view, it has never really worked well enough. Kindle's landscape viewing mode is usually better than reflowed PDF content.
By contrast, my Xoom tablet (1280x800) is GREAT for PDF viewing. Ironically, the reflowable formats tend not to be as pleasant, in part because many of the reading apps are not yet optimized for large screens (e.g. no margin adjustment or 2-column-landscape option), and images prepared for small screens are too small and most apps don't let you zoom them. When I have a choice between ePub and PDF, I usually pick PDF.
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