Alex Manchester, from Step Two Designs has a very useful article on when to publish Intranet content in PDF format rather than HTML. I agree with Alex's point that PDF is suboptimal for most content because of several limitations (most of them around the additional overhead in editing and reading the document) but still has its place: like for documents that are distributed for printing.
Too often PDF serves as a crutch for users with limited web content management tools and skills. For many, it is easier to save a MS Word document as a PDF and upload it than to work with HTML (either through a CMS or using an HTML editor). The real cost of using PDF occurs after the content is published when users have to wait for Acrobat to load only to find that the document is not what they are looking for and when the document needs to be updated but the original Word document has been lost. I think the most painful abuse is the case where the company has a wiki and users upload MS Word and PDF files as attachments rather than edit the content in the pages. Doing this degrades your wiki into a poor man's shared drive — and that is very poor.