The YOUMoz section of SEOMoz (http://www.seomoz.org/ugc/how-to-optimize-pdf-documents-for-search) recently posted a checklist for performing SEO on PDFs, which is where I got much of this material. As with any checklist, the devil's in the details. It starts with search-friendly file names. You make sure the file names of your other web pages are useful to searchers who find them in the SERPs, so don't call it 1234.pdf, call it (for example) GrowTomatoes.pdf.
Tackle your PDF's title tag in the same way. You optimize the tile tags of other web pages, so why not this one? Hold yourself to the same character limits as you would for the title tag of any other web page.
If you're using Adobe Acrobat, you'll get a description field. This translates to the meta description of a web page, and will be displayed in the SERPs under your title tag. Treat this as you would the meta description for any other web page; if you use them, keep it informative and concise, so your readers will really know what they're getting when they click on the link.
Again, if you're using Acrobat, there's a way to view “Additional Metadata.” You'll find additional fields to fill out there. Some search engines may rank some of these fields, so you may want to fill them out completely. After this, you'll want to hit the Advanced menu and find the sub-menu for Accessibility. This is great if you want to help visitors with screen readers and magnifiers read your PDFs.
Do you use Alt tags on your regular web pages? Believe it or not, there are also ways to do this with images in your PDFs. Check your program. It's another way to help the search engine spiders get a better handle on what your document is all about.
Okay, so you've added all of the “on-site” details that you would to any web page; how about the “off-site” details? I'm talking about links. You'll definitely want to add a link in the document back to your website, for both the search engine spiders and your human readers. If other websites decide to host a copy of your PDF, that link in the document becomes a backlink to your website.
For obvious reasons, you won't want others to be able to easily remove that link – or otherwise edit your PDF. So make sure you write-protect it before putting it online.
Finally, you may feel certain that a PDF is the best way to offer your material, but not everyone who visits your website will agree with you. It's always a good idea to offer different options to your visitors. So you might want to present HTML versions of your PDF documents. Many web surfers find them less of a hassle than clicking on a PDF and opening a reader when they just want to casually browse your site. If they like what they see in HTML, though, they may go to the PDF version to print it out later. So different formats are good for different purposes, and it's helpful to your visitors – both humans and search engine spiders – to have more than one available.