The way I see it, there are two kinds of people who create lengthy PDF files: Those who include bookmarks, and those who don’t.
The individuals who neglect to add bookmarks (and I’m sure this couldn’t be you, because you would never do anything like that) put their readers through inconceivable inconvenience; when those readers need to scroll page by page until they get to chapter 23, they’ll be cursing the document author all the while. I’m sure the first 22 chapters were just fascinating to glance at as they flipped by, but when all these poor readers need is a particular paragraph, it can be a pain in the neck to try and find it without bookmarks.
Now, those of us who do add bookmarks to our PDF files know exactly why it’s a good idea to do so: not only can you mark pages for your own use and come back to them later, you’re doing a favor for anyone who will be reading the PDF file and needs to skip straight to chapter 23. And then back to Chapter 16. And then on to Chapter 144. With bookmarks, you’re empowering your readers to navigate a PDF file just like they might a website or an ebook: with one easy click.
What you might not know is that adding bookmarks actually improves the functionality and accessibility of your PDF documents. Your bookmarks honor the view you were in when you made the bookmark, so when you click it you’ll be taken straight back to the page, section, and magnification you were at originally. You can also use bookmarks to split a PDF file into component pages or chapters. Whoa! All of a sudden, your PDF is structurally intelligent!
There are all kinds of ways to use bookmarks with Adobe Acrobat beyond just marking pages (although that’s still a nice thing to do for your readers); check out these tutorials and Q&A at AcrobatUsers.com (you can also post your own question to get an Acrobat expert’s help). You’ll be making structured, navigable PDF files by the end of the day.