From Gnome 2.14 on, configuration files for gdm moved from a single /etc/X11/gdm/gdm.conf to a split between /usr/share/gdm/defaults.conf and /etc/X11/gdm/custom.conf. The exception to this is if a user has an existing, customized /etc/X11/gdm/gdm.conf, custom.conf will be ignored. This was done by upstream to keep users from losing settings since there wasn't sufficient time to write migration code -- reference Gnome bug 333327. This occasionally results in users editing custom.conf but not realizing they need to delete gdm.conf, so their settings are not applied. Going into 2.16, there is still no migration code. Brian Cameron suggests in the above bug that the best approach is for individual distros to rename gdm.conf to custom.conf, overwriting any existing custom.conf as it would simply be ignored anyway. This should be done during the 2.14->2.16 upgrade. It would probably be a good idea to throw comments into the renamed file indicating what happened and what the new config file setup is, as well as an einfo message to the same effect. This bug should block the 2.16 tracker.
Okay, I've just committed 2.16.1 with code to move gdm.conf out of the way. This gets you default settings, but we've had several reports (it bit me too) of a legacy gdm.conf causing gdm to fail to start.