PDF and HTML
Jeff Atwood's "The Trouble with PDFs" post lists advanced layout as the virtue of PDF, but as he points out, there isn't much these days that you can do with PDF when it comes to layout that you can't do with HTML and CSS.
The real benefit to PDF as far as I'm concerned is that you can save the thing to disk.
Many downloaded products these days offer HTML based documentation through a link to their site. To the end user, this means that if the site is down, or their connection to the internet is offline, they don't have access to that material.
There is no standard way of offering a single file download of a collection of HTML pages that you can just double-click on to view. You can offer a *.zip file containing the contents of your site, but then the user must extract the whole thing somewhere and know to open index.html (or whatever the start page is called). You can create a *.chm file, but that's an Internet Explorer specific format.
A PDF is a timeless representation of a stack of pages. I have the owner's manual for my stove in PDF format, as well as my cordless phone, universal remote, and a bunch of other things. I like knowing that I'll still be able to view those in 10 years, when there's a good chance I won't be able to find the original content online anymore.
I'm OK with PDF as an output format - that's what PDF is after all, you can't hand-edit a PDF - so creating HTML for online viewing and a PDF for offline viewing from the same content is a great way to go.
(And with Acrobat, you don't even need the site author to offer the PDF to download - You can hand Acrobat an URL and it will walk links and build a PDF for you from the site. It won't be as pretty as something authored for PDF but if you're looking to archive some content, it works pretty well).