The Winform application is release with ClickOnce in our Intranet. We store personal preference for the GUI in the Isolated Storage. All works pretty fine :)
The pro
a summary from the other answers:
IsolatedStorageFile isolatedStorage = IsolatedStorageFile.GetUserStoreForAssembly();//for visual studio
if (System.Deployment.Application.ApplicationDeployment.IsNetworkDeployed)
{
isolatedStorage = IsolatedStorageFile.GetUserStoreForApplication();//for click once applications
}