Jakob Nielsen's recent diatribe against PDF for online viewing did strike a nerve among PDF developers. That's too bad. Since he incorrectly ascribes the problems he identifies to the PDF format rather than the authorship, Nielsen misses his own point. The only real culprits (and it is ever so, no matter the format) are the authors - and the attention authors pay to ease of use considerations. Ignoring this vital distinction, Nielsen does his readers no favors.
The following guidelines for PDF authoring may not help you entirely avoid Nielsen's evil eye, but the vast majority of your users and readers will be thankful nonetheless. Take good care of your PDFs when you make them, and everyone who ever uses the file will thank you for your consideration.
If the document is very long, offer "chapter" or "article" PDFs in addition to a single file for the entire document.
If you add bookmarks, congratulations! You are an educated PDF publisher! Then ... make SURE you set the PDF Inital View to show "Bookmarks Panel and Page". Otherwise most users will have no idea they are there at all.
Files greater than 10 pages in length should ideally include bookmarks.
Files greater than 20 pages in length MUST include bookmarks, or your readers will be unappreciatively stuck flipping pages.
Include web links on your PDFs to return to your Web site. 99.9% of PDF files do NOT include this feature.
Avoid 2 (or more) column text on your documents unless absolutely necessary. If you do use more than 1 column, consider the Article Threads feature to ensure easier readability.
Always indicate the size of the file so users can make an informed decision about downloading it.
Always ensure that files are "Optimized for Fast Web View" (exception: files containing form-fields shoud NOT be optomized for Fast Web View.)
Ensure that the server hosting the files supports Fast Web View. Most do automatically.
Ensure the file is as small as possible. PDF files are frequently WAY overweight.
OK, so you want to stamp your document. Maybe you need to give reviewers some advice about the document's status or sensitivity. This tip from author Ted Padova demonstrates how to add stamps with the Stamp Tool along with related comments.