First, MS Office apps and Adobe CS apps can all save to PDF now. It's not always the best way to make them, but in the case of Office, you often get some nice automatic enhancements, especially if the source document is designed semantically with accessibility in mind.
At TPS we use Acrobat Pro for users who need to make annotations and do basic editing (rotate, replace page, etc.). Acrobat Pro also gives you Distiller, which lets you set a watched folder to turn valid .ps files into PDFs and apply any embedded PDFMark code to create enhancements. There's a nice set of samples in the Pro fileset, which can be found on the CD if they don't install for some reason. Among these is are samples for PDFMark concatenation, bookmark and hyperlink, all of which are described in more detail in the Adobe "pdfmark Reference Manual," and which are governed by information in the Postscript Language Reference (aka "the red book"). Note: Distiller is licensed for a single user, but can work well beyond the license's limitations, provided your applications allow PDF processing jobs to finish before collecting the resulting files, and you overcome the limitations of it not being a server product.
The gold standard for PDF creation is the ActivePDF product set. For most of us they are prohibitively expensive, but the university may have a license already with some of the enterprise applications.
David Pepper, M.S.
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