I often use an SQL table to hold my application settings. I create a singleton class, ususally called AppSettings, that I load with data from the table. The AppSettings class is then used to get the config values instead of directly accessing the config files. For ASP.Net apps, I instantiate the AppSettings class in the Application_Start event in Global.asax.cs.
Doing this gives me a way to allow the user to control some of the app settings, e.g. an email address for notifications. It also can simplify things when maintaining prod, QA, and dev versions of the app (assuming you have separate database instances for each)