In newer releases you can set this also from the preferences (⌘,). If you are using the X11 version shipped with OS X, you can most probably just replace org.macosforge.xquartz.x11 with com.apple.x11.
defaults write org.macosforge.xquartz.X11 wm_click_through -bool true
defaults write org.macosforge.xquartz.X11 wm_ffm -bool false
Getting halfway sane mouse click behaviour in Gimp on OS X
I can definitely recommend the X11 packages from the XQuartz project. They are more up to date than the X11 server shipped with OS X. Also, the Gimp packages over at Lisanet are fantastic, too. However, the default click behaviour of X11 or rather quartz-wm is not optimal, especially for the Gimp. Usually I like focus follows mouse, but for an interface like the Gimp, it does not make sense. You always inadvertendly focus on an image, that you did not want to focus. Since there is no delayed ffm mode in quartz-wm, I opted for click-to-focus instead. However, quartz-wm swallows mouse clicks on inactive windows. This is also not worthwile for the Gimp with it's extra tool palette windows. So the soluation is: click-through combined with click-to-focus. Easy: