Gtk allows the grouping of windows, but this grouping does not allow for 
other applications (example: window manager) to work with the groups. Gtk 
gives all windows in the application the same group leader hint, regardless 
of their actual group.

Bug #116004 and #115994 are two examples of this problem.

Being able to work with a group of windows at a time make the Gtk MDI 
interface much more pleasant to work with, as you can raise all your gimp 
windows to the front by only clicking one of them. No more losing one dock 
somewhere behind a terminal window.

On the other hand, being forced into the behavior for all Gtk apps is 
clearly wrong, for apps like nautilus and galeon. But there is no way to 
distinguish between the two cases for me. The applications need to be able 
to group their windows appropriately.