I found that if I kill and restart quartz-wm then the hidden applications will reappear. Having had this happen to me several times, I came up with this quick fix. First, make a backup copy of /etc/X11/xinit/xinitrc. Next, using sudo, edit the original, replacing this line at the bottom of the file:
exec quartz-wm
with this:
while :
do
quartz-wm
sleep 5
done
Restart X11 after you make this change. Now, the next time the Finder dies/restarts and you find yourself with missing X11 windows, either open a new xterm from X11, or launch Terminal and run this on the command line:
ps -ax | grep [q]uartz-wm | awk '{print $1}' | xargs kill
This finds the process id (pid) of quartz-wm (and skips the pid of grep) and sends it to kill. In five seconds, quartz-wm will restart and all of your missing X11 apps should reappear. If this doesn't happen, then you have stubborn quartz-wm that doesn't want to die. Just repeat, but add the -KILL (same as -9) option to kill:
ps -ax | grep [q]uartz-wm | awk '{print $1}' | xargs kill -KILL
Note: If you mess up your xinitrc file, just use Terminal.app to copy your backup back into place and try again.

