The word is - "Java on Vista: Yes, it Works"
Some folks have noticed that when they run Java applets in the browser, that Aero and desktop composition would get disabled. This was due to Java locking the primary buffer, and when that happens, the DWM no longer has access to the resources needed to draw the desktop, therefore we disable desktop composition. Sun has since addressed this issue, as you can see in this post in Chet Haase's blog. Chet also provides lots more detail about what was up, what version it's fixed in, and when it will be available - or, as BubbleMan insists on saying, availabubble.
And while we're on the topic, earlier versions of Apple's QuickTime/iTunes also exhibited this primary-locking behavior. The lastest updates to QuickTime/iTunes no longer does this.