Two Perl scripts are now available:
Script 1 - For downloading PDF files to be saved using their unique PubMed ID number. Requires a local web server (eg Apache or PWS) and Perl. This script should be placed so it can be found by http://127.0.0.1/cgi-bin/pmget5.cgi, which is the 'PDF' link in the search results. I also think there must be a better way of doing this, as it doesn't work if you need to log in for fulltext access.
Script 2 (by email) - For tagging PDF files with metadata describing the title, author, keywords and journal details (for use in PDF Explorer). Requires files to be named using their PubMed ID number (see Script 1 above). Also requires Windows, Perl and Acrobat 5. Mac/Applescript version to come.