For a while now I have been using Zotero on Firefox to handle researching topics. It also allows PDF indexing, but for this you need to set some things up first. Start by installing xpdf from ports, it’s located under graphics/xpdf. This will install pdfinfo and pdftotext amongst others. Next go to your Zotero data directory, by default this is the zotero directory under your profile directory in $HOME/.mozilla/firefox, and create two symbolic links pdfinfo-`uname -s`-`uname -m` and pdftotext-`uname -s`-`uname -m` which will point to /usr/local/bin/pdfinfo and /usr/local/bin/pdftotext, respectively.
Now, when you restart Firefox, Zotero should be able to pick up the files. Check by going into Zotero’s preferences and navigate to the Search tab. It should state something to the effect of pdftotext version UNKNOWN is installed.
