I'm with torifile on this one.
I was finally able to find and download the standalone installers for gimp and x11 - they can indeed make for a real messy situation.
The "archive and install" option would be your best choice, for the very same reasons he mentioned. That'll be much easier than having to manually pick out the files and folders that have been changed.
Regarding GIMP, here's my opinion. It is a good program, but you get what you pay for. Hint: it's free. So, you can't expect it to work perfectly in *all* environments. I've used both Photoshop 7 and GIMP and I greatly prefer Photoshop. GIMP's non-native interface is enough to irk me, but coupled with some unfamiliar functions and often slow behavior, it isn't good enough for me to use regularly. I only have it on my system for testing purposes.
So, why is it that I haven't experienced any of the same problems? It might be that I had used the "fink" installation of X11 and GIMP. As torifile also mentioned, fink installs files in a custom directory, separate from the other system files.
Well, best of luck with the reinstall!