From a recent post on the Apple Java Development mailing list:

Is it just me or did the shortcut key to the preferences menu disapear with Java 1.4.2? Is this an api change, some kind of ui guideline issue, my imagining things, or Apple just randomly deciding to change things?

I'm really, really not impressed with Apple's Java support now. I mean, sure, I'm still impressed and excited to know that Java 2 ships with OS X out of the box, and that any Mac running OS X from 10.0 on up has it. At the same time, the people doing the hacking of things that aren't obvious no-brainers need to stop changing their collective mind about everything else [that's not a no-brainer]. Apple's already changed the way Java apps handle the Apple specific application menu (Preferences, About [this app], Quit [this app], etc on the top left of the menu bar) and how they want you to package apps so that they look like a native, double-clickable executable.

I don't care how bone-headed the implementation is, but they really need to stick to their guns for more than a couple of years at a time. And, as pointed out above, when they break things they 1.) shouldn't do it so that the old way is automatically gone and 2.) should warn their developers.