How about WBEM?
Sorry for the long posting, but it's really a matter of heart to me...
The problem with configuring (not only) applications has multiple dimensions. One of them - as already pointed out in different posts - is access technology. A single, consistent method is necessary to read and update all the configuration data. I chose the term "access technology" deliberately because we cannot not really expect all the legacy /etc files like inittab and passwd to go away or change their format (be it XML or something entirely different). We also cannot faithfully expect that formats converge, meaning one is given up in favor of the other. This means that the access technology must facilitate a wrappering approach to the current configuration repositories. It also has to be suited for scripting, fancy GUIs of course and allow remote access, especially important if we think of bigger installations.
Coming up with such a technology is conceivable, it will buy us only part of the solution however. The problem is that even if all config data was accessible in a single way, we are still missing semantical information (ever tried to configure a printer via, say the Windows registry?). What this really means is that a data model is needed in addition, describing the semantics of configuration data (and other parts of the system). The data model must provide different levels of detail, giving the possibility to perform high-level, generic configuration tasks as well as highly application-specific modifications.
Let's take web browsers as an example: all of them allow the specification of proxy servers, each in it's unique way. Now assume a situation were a company-wide proxy server changes and hundreds of clients have to be reconfigured to reflect the change. In this case it's really convenient perform a remote "set proxy for client xyz" configuration command, without even knowing the exact nature of the client's browser.
Access and data modeling technologies for systems management purposes exist today already, in form of DMTF's WBEM and CIM standards. Parts of the data models therein deal with configurations and settings (of devices and applications) which I believe to be a sound base for further developments. Now what does this mean? For the purpose of application configuration, appropriate data models have to defined by extending the respective CIM models. Then it is necessary to write data access modules interfacing to the real resources, the so called providers. And what's perhaps most important, management applications exploiting the stuff.
Several Open Source projects related WBEM technology are cooperating under the umbrella of the WBEMsource initiative. If you want to learn more about, http://www.opengroup.org/wbemsource would be a good starting point, as well as the DMTF website http://www.dmtf.org . To summarize and emphasize my statement: the infrastructure technology is there, the hard work still has to be done. It will take quite some time, but if successful it will lead a way out of all the configuration quirks and nightmares, and this not only for Linux but for all platforms supporting WBEM.