Apple has released a "Java Update for Mac OS X 10.3.9" via Software Update utility :

This update will correct issues affecting some Java users following the
installation of Mac OS X v10.3.9 Software Update.

For detailed information on this Update, please visit this website:
http://www.info.apple.com/kbnum/n301382

Earlier this week, Apple acknowledged the issue by posting a support document showing how to fix it manually.