Amplify to autotag (Score 1)

Once you OCR all your paper (FineReader is not bad), and full-text index your PDFs (Beagle for Linux, MOSS for Windows), you'll still have a problem with narrowing down a keyword search. Try Amplify http://www.hapax.com/amplify.php on the title/abstract/methods page of each document and maybe you'll get useful metadata.