Not all PDFs are created equal—just ask any prepress manager. With Adobe Acrobat offering so many versions of PDF documents, and so many options for creating them, it's hard to know what you need to do to prepare a truly press-ready PDF.

Layers Magazine has a great article on creating perfect pre-press ready PDFs for print designers.

For what it's worth, I stick with PDF/X-1a for my PDF output. PDF/X-1a creates a "dumb" PDF that will work on virtually all PDF-capable RIPs by removing all transparency, embedding fonts and basically offering the least amount of options in your PDF file.

To brush-up on the various PDF formats, you can take a look at this post I made a while back which features a brief description of each format.