currently gconf always depends on gtk, although it is only needed for a small sample applet. There I added a gtk-useflag to the gconf-2.12.1.ebuild in portage, so that gtk (which depends on X) is optional. This is especially useful, as e.g. ebox depends on gconf and you don't want X on your server, do you? This ebuild is likely to need files from the files-dir of gconf from the tree.
Created attachment 80436 [details] gconf-2.12.1.ebuild
I agree with your statements, and ideally gconf should have the 'gtk' flag, but we force it for now so it doesn't break other applications which rely on stuff provided only if gconf was compiled with gtk support. See bug #100238 for an example. The right solution would be more in the lines of implementing USE-aware dependency atoms in portage, but until that day arrives, this will have to wait.
I don't think that somebody who'd like to use gconf without gtk would be interested in any graphical (gnome) programme, so what other non-X programms depend on gconf with gtk enabled?
