The main thing is to make sure all the PDFs are well branded so that when someone downloads the PDF, they can easily find your site if they want to see if you have similar things on related subjects – and, of course, even if they don’t visit the site, if the

PDF is branded – there’s a brand impression for you.
For me, though, I tend to make an HTML version of important PDF files. Sure – allow them the download still – but do the best I can to provide the same thing as an “in-browser” experience. Google will tend to favor the HTML version in most cases – especially if (near the beginning) you’re offering up the PDF version as an alternative.

Still, for me – from a digital marketing perspective more than a pure SEO perspective – brand the hell out of your PDF downloads. Those things get handed and/or printed out for proposals, training sessions, and sorts of things.

And, of those PDF files get posted elsewhere, even though the links in them are treated as nofollow – there is almost certainly stuff going on that helps establish your brand entity and its relationship to the things within the document(s).