An excellent tip (though it seems to have been around for a while) from the Gimp.app readme:
defaults write com.apple.x11 wm_ffm trueenables 'focus follows mouse" in X11 (using the default Aqua-style quartz-wm window manager), which means you don't have to go to all the trouble of installing Apple's Developer Tools, Fink and Blackbox just to get usable Gimp windows.