1. Make sure your PDFs are text-based
2. Complete the document properties
3. Optimize the copy
4. Build links into PDF
5. Pay attention to the version
6. Optimize the file size for search
7. Pay attention to placement
8. Influence meta descriptions for PDFs
9. Specify the reading order
10. Tag your PDFs
11. 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.