Something I always get stuck on, making PDFs that are properly functional. Inparticular, making those snazzy left side bookmarks that jump out when the file is loaded (great for instruction manuals, books etc)..

4) Add bookmarks
Bookmarks act as a table of contents in a PDF file, allowing users to quickly navigate a PDF. Who has time to scroll through 36 pages in a PDF file to find chapter 3? For PDF files larger than two pages, add bookmarks to the file.If you followed step 2 (save/export document as tagged PDF) bookmarks will automatically be created from the source document. If the Word source document contained a table of contents, the table of contents will display in the Bookmarks pane.

To create bookmarks, open the Bookmark Panel (View > Navigation Panels > Bookmarks or select the Bookmark icon in the navigation pane). Use one of the following methods:

  1. Add bookmarks based on document structure – the easiest method!
    1. If the PDF file is tagged, you’re in luck! Use the structure to create the bookmarks automatically
    2. In the Bookmark pane, select the Options menu
    3. Choose New Bookmarks from Structure
    4. The Structure Element dialog box displays – select the elements you want to convert
    5. Select OK
  2. Create bookmarks from selected text in the PDF file
    1. Use the Select tool from the Select and Zoom toolbar
    2. Select text you want for the bookmark
    3. Select the New Bookmark icon on the Bookmarks pane toolbar or in the Options menu, select New Bookmark to add the text
  3. Add blank bookmarks and fill them in manually – most time consuming
    1. In the existing bookmarks, click the location above where you want to add a new bookmark
    2. Select the New Bookmark icon on the Bookmarks pane toolbar or in the Options menu, select New Bookmark
    3. The bookmark will be created with the default text “Untitled”
    4. Enter the text for the bookmark

Heres the full article to the top ten hints about making great PDFs, check it out, well worth a read and a bookmark

http://refresh-detroit.org/2008/12/02/ten-tips-for-creating-usable-and-accessible-pdfs/