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It depends on whether the setting you have chosen is at "User" scope or "Application" scope.
User scope settings are stored in
C:\Documents and Settings\ username \Local Settings\Application Data\ ApplicationName
You can read/write them at runtime.
For Vista and Windows 7, folder is
C:\Users\ username \AppData\Local\ ApplicationName
or
C:\Users\ username \AppData\Roaming\ ApplicationName
Application scope settings are saved in AppName.exe.config and they are readonly at runtime.
Two files: 1) An app.config or web.config file. The settings her can be customized after build with a text editer. 2) The settings.designer.cs file. This file has autogenerated code to load the setting from the config file, but a default value is also present in case the config file does not have the particular setting.