The combo update which is supposed to fix the problem with partially installed X11.app is actually exposing it. If you gradually upgrade from 10.5 to 10.5.1, then to 10.5.2, then to 10.5.3 and finally to 10.5.4 your X11 server will still work OK. But should you make the mistake and take a too big leap i.e. from 10.5 to >= 10.5.2, your X11 is screwed.

It turns out that you can still restore your X11.app without going through the whole system reinstall and then applying the gradual upgrades. Just install the community supported XQuartz and keep it until Apple fix their combo update (may be in 10.5.5 combo, who knows?). Rumor has it that XQuartz is actually better than the Apple’s one ;)