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

W3C guide on creating accessible pdf documents.

'Tagged PDF is a stylized use of PDF that allows reliable recovery of text, graphics, and images in PDF documents, with no ambiguity about the contents or the ordering of the contents. A Tagged PDF file is page oriented. Each page of a Tagged PDF document contains the text, graphics, and images in reading order, as determined by the authoring application. A Tagged PDF is a Logical Structured PDF. Logical Structure is used to carry information necessary to support tagging for access and content extraction, as well as styling properties needed for access, reflow, and content extraction. It also provides the identification of the article flows in the cross-page environment for access and content extraction.'