I think Mac OS 10.3.9 is the first system update I've had that made my computer less functional. That's not something I can say of my experience with Windows (where I often lose functionality), so I guess I should be glad, but I'm a bit disappointed that Apple hasn't already released an update. If you've installed 10.3.9 and find some of your applications will no longer open, you can solve the problem by re-installing Security Update 2005-002. That worked for me, anyway.
Update: Apple has since released an update that fixes the 10.3.9 Java problem.