Here we tend to use nVivo for qualitative research/analysis. It's pretty robust, but the handling of PDF files leaves a lot to be desired. What nVivo seems to do is to convert the PDF into some sort of RTF-like format. Unfortunately the fidelity of the converted file isn't that good. In fact, it can be darn difficult to work with most converted files if they are anything more than plain-old-text.
The problem is so bad, and I am so keen to analyse/work with PDF files I'm thinking of changing to Atlas/ti. That programme handles PDF files in their native format … there is no loss of fidelity when working with them.
What I can't decide is whether the learning curve/downtime is worth the change.