I have been in charge of setting multiple Linux terminal servers up through the years. I have also been tasked with getting Linux desktops conforming to the same user defaults and centrally manage those. Some applications that behave the *nix way are really easy to manage but the ones like OpenOffice, Firefox, Gnome and others can be a real pain because they have settings in all the different places and with different ways of setting them.
Sometimes i wonder if many developers are very good at programming but perhaps not that up to speed on making them easily managable in a larger enviroment. Its really not that much of a hassle of making it really easy to manage settings for an application.
Put user specific settings in "~./appname", the default user settings in /etc/skel/appname and distributing, altering them en masse and setting sane defaults becomes really easy and does not in any way demand anything else than very simple scripts.
The worst of them all is in my mind Gnome that uses gconf. While i cant comment on its merits for programmers its a living hell managing as an admin where you have more than a couple of computers or on a terminal server. I totally abhorre using any kind of databases or registers for settings. I cant imagine it saves especially much time for the developers and it certainly introduces nothing but troubles for the users.
This is in my mind really something that needs to be taken into consideration for those who wish people in corporations using their apps more. Especially firefox and openoffice thats pretty hard to manage on both Linux and Windows regardless of any policy tools , scripts or whatnot.
Linux in itself and as an OS works wonderfully in regards to settings and such, its just some of the applications bolted ontop and ran on Linux that would really need some rethinking from a management point of view.