Search engine land has posted a useful article on the key things to do in order to optimize PDFs for search engines.
Here's an overview:
- Make sure your PDFs are text-based
- Complete the document properties
- Optimize the copy
- Build links into PDF
- Pay attention to the version
- Optimize the file size for search
- Pay attention to placement
- Influence meta descriptions for PDFs
- Specify the reading order
- Tag your PDFs
- Pay attention
There are a few recommendations here that I was unaware of, such as specifying the reading order and adding tags.
Given that #1 is a no-brainer, at the very least I would recommend doing 2 and 6 in order to put your PDFs into some sort of minimum fit state for search engine accessibility.