For me, at least, it was 100% reproducible using nothing but OS X. Just had to use Apple's Java and run Minecraft in it, and toggle full-screen mode a few times. Then it got fixed, I think around 10.8.3 or 10.8.4, and after that I have had no problems whatsoever.
So for me, it appears to have been Apple's video driver, not any third-party plugins or anything.
Ultimately, it comes down to this:
If user code can cause the system to hang, there is a bug in the kernel. Period. It doesn't matter whether it's Java, or Flash, or whatever else; if any sequence of bytes executing as a non-root user can cause the system to hang, the kernel has failed in its primary job.
Luckily, Apple tracked down and fixed the instance that was affecting me.