Apple released X11 Update 2006 yesterday. Soon after installing X11 on my PowerBook, I noted an annoying bug: when you switched X11 into the foreground using Alt-Tab, none of its actual windows would come with it. That is, you would get the X11 menu bar, but the windows themselves needed to be manually brought to the foreground. X11 Update 2006 has fixed this, albeit 12 months later.
I also noted that Emacs-over-X was disappearing with some obscure X Windows protocol error. I assume this was an issue with Apple's implementation, but I'm not certain. I've certainly never seen it anywhere else. I've had Emacs running over X for about 10 minutes now, and it hasn't died yet. So they may have fixed two bugs.