Search engines can crawl & index PDF files. For optimizing PDF files few point are worth considering.

1. Use keywords enrich contents in the PDF file.

2. Proper use of <H1><b><I> should be in the PDF file.

3. Targeted keywords should be included in the page urls.

4. Use Acrobat 6.0 or above version for creating PDF files.

5. Dont use too much graphics/images in PDF files.

6. Keep PDF files length as less as possible.

These are some tips from my side.