I really do think applications should try to zero-in on a few standard configuration file formats - I really don't have a strong preference on one (although avoiding XML would be nice). It makes the system uniform and makes it easier to move between applications. Of course, applications can add extended sections to suit their need.
Another related point is the location of configuration files - standard Linux/Unix has a nice hierarchy /etc/ for and /usr/local/etc and others for user-specific configurations (I'm sure Windows and OS X should have a similar hierarchy too) but different applications still end up placing their configuration files in unintuitive places.
I find this lack of uniformity disturbing - especially because it looks so easy (at least on the surface) to fix and the benefits would be nice - easier to learn and scriptable.
A last unrelated point - I don't see why Linux distributions cannot standardize around a common repository - Debian and Ubuntu both share several packages but are yet forced to maintain separate package databases and you can't easily mix and match packages between them. This replication of effort seems more ideological than pragmatic (of course, there probably are some practical reasons too). But I can't see why we can't all pool resources and share a common 'universal' application repository - maybe divide it into 'Free', 'Non-Free', 'Contrib/AUR' like granular divisions so users have full freedom to choose the packages they want.
Like other things, I think these ideas have been implemented before but I'm a little disappointed these haven't made it into 'mainstream' OS userlands yet.