I've written a small script which is far from being finished, but it should work in the current stage. You might find it handy if you're using Latex for your article or thesis: Simply give it your bibtex-file (your bibliography) together with your email address and you will receive email-alerts in the future whenever one of the articles from your bibliography is cited by one of the ~800 journals from Highwire.org.

The current script only works on articles from NAR/Bioinformatics, but it should be easy to modify that. It requires wget, which is available for Windows with cygwin. For a free citation manager with direct Pubmed-access which manages your BibTex-files, have a look at
http://jabref.sourceforge.net

URL

http://www.stud.uni-potsdam.de/~haussler/master/masscitetracker-0.5.pl