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[5001] Xquartz: bootstrap_look_up(): Unknown service name
org.x.startx[5001] giving up.
org.x.startx[5001] /usr/X11/bin/xinit: Operation timed out (errno 60): unable to connect to X server
org.x.startx[5001] /usr/X11/bin/xinit: No such process (errno 3): Server error.
org.x.startx[5164] font_cache: Scanning user font directories to generate X11 font caches
org.x.startx[5164] font_cache: Updating FC cache
org.x.privileged_startx[1606] font_cache: Scanning system font directories to generate X11 font caches
defaults[5191]
The domain/default pair of (org.x.X11, dpi) does not exist
org.x.startx[5164] xauth: creating new authority file /Users/scott/.serverauth.5164
org.x.startx[5164] Xquartz: X11.app = /Applications/Utilities/X11.app/Contents/MacOS/X11
org.x.startx[5164] Xquartz: Starting X server: /Applications/Utilities/X11.app/Contents/MacOS/X11 --listenonly
org.x.startx[5164] dyld: Library not loaded: /usr/X11/lib/libpixman-1.0.dylib
org.x.startx[5164] Referenced from: /Applications/Utilities/X11.app/Contents/MacOS/X11.bin
org.x.startx[5164] 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[1606] font_cache: Updating FC cache
org.x.startx[5164] font_cache: Done
org.x.startx[5164] waiting for X server to begin accepting connections
By the way, Snow Leopard users are not affected by this problem.