GIMP is a great program, but I always found it was a bit annoying to use on OS X (Leopard). First of all, whenever X11 starts, a new xterm window along with it. Besides that, when switching windows you need two clicks before GIMP (or any other program, really) registers the click and actually does something - the first click just switches the active window. Seeing as GIMP has it's tool palette in a separate window, this quickly became extremely irritating.
After a quick google, I found many sources saying that to disable xterm, I needed to copy /private/etc/X11/xinit/xinitrc to ~/.xinitrc and edit out the "xterm &" line inside. That's easy enough, but the only problem is that on Leopard with the latest X11 from XQuartz (18.104.22.168 at the time of writing) installed, /private/etc/X11/xinit/xinitrc doesn't exist! Although /usr/X11/lib/X11/xinit/xinitrc does, editing out all references to xterm doesn't work anyways. Instead, the app_to_run preference needs to be modified:
defaults write org.x.X11 app_to_run /usr/bin/true
/usr/bin/true is a command that does nothing (literally), so this essentially tells X11 to autostart nothing. I moved onto my next problem and found that to solve the two-clicks problem, the solution was to enable the "focus follows mouse" option like this:
defaults write org.x.x11 FocusFollowsMouse -string YES
I've been using that for a few months and I find it's still pretty annoying, but it's still less annoying than having to click twice on everything. Fortunately, I recently discovered the "wm_click_through" preference which is exactly what I had been looking for all along:
defaults write org.x.x11 FocusFollowsMouse -string NO
defaults write org.x.X11 wm_click_through -bool true
Now X11's window focus is back to normal, and clicking on inactive windows works as expected; it switches the window and activates the widget you clicked on. Problems solved!