Many of them come down to preferences, what settings you say, when you need access to the settings, and how often they will change.
As a rule, I try to make my web.config and app.config pretty small. Settings for infrastructure things (for example, modules for loading, linking, log settings, ORM settings, etc.). All I really need or need to have access to App_start or my Main () method, basically.
Something more complex or applicable to a smaller part of the application, etc., I usually do not put in the configuration files, but instead I have settings objects that I insert through my IoC container, or pull them out of the database.
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