I have a class library that is usually called from a .net console or web application. It integrates with various components, and relies on an app.config or web.config.
I
You can always include additional sections within config files. In your ipy.exe.config file you can add an include to import external config settings; say myApp.config.
In a batch/command file you can always copy over a specific .config set into myApp.config and therefore run with different config files on demand.
Have a peek at this blog on how to achieve this; http://weblogs.asp.net/pwilson/archive/2003/04/09/5261.aspx