Hello, EndNoter.
You can import a whole folder of PDFs, though if they’re too old they may not have DOI numbers, which are necessary for EndNote to be able to locate the reference information for each PDF.
To learn more about importing PDFs, please see the video here: http://youtu.be/lHv_U6hZczM and the knowledge base article here: http://endnote.com/kb/108622