My own experience is that I prefer PDFs when I'm making my own ebooks, but EPUB when purchasing ebooks produced by others. Since the ebook creator has to deal with so many screen options when producing an ebook, EPUB allows him/her to create one ebook that can be acceptably viewed on any ebook reader. That is something that is difficult, if not impossible, with PDF.
The reason that I prefer PDF when making my own ebooks is that I can format them specifically for my ereader and they will look exactly on my ebook reader as intended. Plus, I use OpenOffice to make my ebooks and I've found using it to make a PDF ebook is much easier than using it to make an EPUB ebook. Plus, reformatting them for different screen sizes is just a matter of changing the page size in the source document.
However, if I was creating an ebook for others I would format it as an EPUB for the reasons in the first paragraph. PDF is good for certain uses, but not for ebooks meant to be used on all ebook readers.
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