"3. Hierarchy and discovery: in Windows or OS X, the preference system has the concept of user, system and domain config so you can set sane defaults at the domain level but a user can still override one of them just for their account. (There's another interesting tangent here where it's useful to have config supplied with a package which can be selectively overridden by a sysadmin without forking the entire file)"
On *nix, system-wide config files are usually under /etc, and they can be often be overridden by dotfiles in a user's home directory.
One example of a way a user can override global/system configs without forking the entire file is using ~/.Xdefaults.
I hear you about there being no common standard, however. It would be nice if there was one good config file format to rule them all, that could please everyone.
But, since you can't please everyone, it's better to have choice than to have someone's (Microsoft's/Apple's/Ubuntu's) idea of "good" forced down everyone's throat.