I always forget to do this. Long ago I installed XQuartz on my Mac OS X 10.5 (Leopard) desktop. For the life of me, I can't remember why I installed it. XQuartz replaces the X11 that comes with Mac OS X. I might have done this since XQuartz is more up to date than Apple's X11. Another possibility is that one of the two X11 apps I use frequently (Gimp or Wireshark) required the update. The reason doesn't really matter, the important thing is to remember to reinstall XQuartz after every Apple Software Update.
If you're experiencing this problem, you might see something like the following in your log files:
org.x.startx Xquartz: bootstrap_look_up(): Unknown service name org.x.startx giving up. org.x.startx /usr/X11/bin/xinit: Operation timed out (errno 60): unable to connect to X server org.x.startx /usr/X11/bin/xinit: No such process (errno 3): Server error. org.x.startx font_cache: Scanning user font directories to generate X11 font caches org.x.startx font_cache: Updating FC cache org.x.privileged_startx font_cache: Scanning system font directories to generate X11 font caches defaults The domain/default pair of (org.x.X11, dpi) does not exist org.x.startx xauth: creating new authority file /Users/scott/.serverauth.5164 org.x.startx Xquartz: X11.app = /Applications/Utilities/X11.app/Contents/MacOS/X11 org.x.startx Xquartz: Starting X server: /Applications/Utilities/X11.app/Contents/MacOS/X11 --listenonly org.x.startx dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib org.x.startx Referenced from: /Applications/Utilities/X11.app/Contents/MacOS/X11.bin org.x.startx Reason: Incompatible library version: X11.bin requires version 15.0.0 or later, but libpixman-1.0.dylib provides version 13.0.0 org.x.privileged_startx font_cache: Updating FC cache org.x.startx font_cache: Done org.x.startx waiting for X server to begin accepting connections
By the way, Snow Leopard users are not affected by this problem.