The first rule of making PDFs is easy… do it in InDesign, don’t even think of doing it in Quark. Navigation, linking to the web and even playing movies can be sorted out in InDesign first before the PDF is made. This way when the client has added his changes these elements don’t have to be re-done just moved.
Take navigation. Everybody loves to click on articles in a contents page to go to that page, or click on an icon to get back to the contents page, or click “next page” or “previous page” to move through the document. Set up a master page in InDesign with a button set to the bookmark of your contents page and left and right “page turners” set to previous page and next page and, bang, you’ve done it! No need to mess around with your PDF in Acrobat Professional tediously setting all the links.