Earlier I read the comic adaptation and I was a little bothered that Gordon flashed the signal at the cathedral instead of the dark sky (as seen in the movie). I took another look at the script and found this:
ON PRESS -- they are quiet. KNOX Question. How do we call him? GORDON He gave us a signal. ON GORDON -- he steps to a searchlight and flips it on. EXT. GOTHAM CITY WIDE - NIGHT On the side of the old cathedral, the BATSIGNAL - the yellow moon, a black-caped man, the melancholy icon calling for help in the dark night of Gotham City.
Obviously the idea came from The Dark Knight Returns. I never liked the idea, glad that it didn't end that way.
It's not a big deal but I thought it was interesting and decided to point it out. One of these days I should read the entire script. It seems like there were a lot of changes and possibly several interesting deleted scenes.