Do you know (or know of) Michael Hughes? If you don't, you should. Mike has all sorts of credentials (if that matters to you)...he also has a wealth of knowledge about usability and writes a column for UXmatters.

And he just wrote a blog post (that I wished I'd written) about how he hates online user manuals that are distributed as PDFs, especially those that are formatted for printing.

If you're going to distribute an online PDF as a user's manual instead of one of the many appropriate online formats, then at least make it easy for your users. Follow Mike's tips: set them up for simplex printing, not duplex. Make the page numbers match up so that page 100 in the PDF uses 100 as the page number that's displayed. Get rid of the "book" overhead like front and back covers.

In addition, I'd add a few more:

• Don't use independent chapter numbering (where each chapter restarts from 1), unless your goal is to frustrate your users beyond belief. (Picture this: you open a PDF that's 300 pages long. You want to read the information in the last chapter before the appendices, which starts on page 6-1. As you look at the vertical scroll bar in the window, where do you think you should scroll to to find page 6-1? To the middle, maybe? To the end? What page number should you go to? Will you find 6-1 on page 100 of the PDF? Page 200? Page 295? Think of how much easier it would be to search for page 200 in a 300-page PDF, especially if page 200 is really the 200th page.)
• Forget "picture-perfect" layouts. I don't mean that you should not care at all, but if your company isn't going to be printing these PDFs for your customers, then relax your standards a little. Don't require that every page element is perfectly placed. If you're not careful, you'll spend more time fixing layout issues and using up the budget before the content is finalized.
• Put the "important but not a priority" stuff at the back. For example, copyright doesn't have to be at the front. Yes, copyright is important (see some of my other posts). But if a user is opening the PDF, it's typically not to read your copyright...it's to find the answer to a question. It's already a harder process than it needs to be because it's a PDF...moving this kind of content to the back makes it easier for the user.

(BTW, I find Mike very credible, even if he does provide quotes from The Gladiator. ;-))