Mac OS X has the CA keystore in /System/Library/Frameworks/JavaVM.framework/Home/lib/security/cacerts. This keystore seems to be overwritten by every Java update, which is very annoying since we have internal CAs for development environments, testing…
Is there a way to preserve keystore changes across Apple JSRs, and now, with Snow Leo JSR3, also across updates for the separate Java developer packages (whose JDKs use the same keystore)?
[ This is outdated info - see the answer below for 10.6+ ]
/System/Library/Frameworks/JavaVM.framework/Home/ is a symlink to Versions/CurrentJDK/Home within JavaVM.framework. Obviously this will change with a new Version. Use the full path (e.g. /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home) and it won't change across updates.