After running the combo 10.3.6 update on my G4 PowerBook, I noticed that one of my Java programs no longer functioned. In fact, running java -version in the Terminal caused a segmentation fault! I eventually broke down and reinstalled Java (first with the Java 1.4.2 base package, and then with the Java 1.4.2 Update 2 package {which includes Update 1}). This fixed the problem.
Having searched around, I eventually found some mention by other folks of a similar circumstances, but they claim they were able to get Java working again by just using the Java 1.4.2 Update 2 package alone.
I hope this saves some other folks some panic!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20041107170431374