Jeepers, my system is riddled with just about every hack possible (save for any SIMBL plugins) and yet I have had no problems at all with the 10.3.9 update. Repaired Permissions after install just as a safeguard, but system was working fine even before doing that.
That being said, I certainly concur with perfessor: run the little java test to make sure it is optimized for your Mac and you'll be pleased as punch with 10.3.9.