Logic.cs

    public partial class App : Application
    {
        private static bool _bIsBlackSkin = true;
        public App()
        {
            Window window = (Window)System.Windows.Markup.XamlReader.Load(new System.IO.FileStream("Window1.xaml", System.IO.FileMode.Open));
            System.Windows.Controls.Button button = ((System.Windows.Controls.Button)window.FindName("ToggleSkin"));
            window.Closed += new EventHandler(window_Closed);
            button.Click +=new RoutedEventHandler(ToggleSkin_Click);
            this.Run(window);
        }

        void window_Closed(object sender, EventArgs e)
        {
            this.Shutdown();
        }

        private void ToggleSkin_Click(object sender, RoutedEventArgs e)
        {
            var rd = new ResourceDictionary();

            string uriSkin;
            if (_bIsBlackSkin)
            {
                uriSkin = @"Skins\Green\GreenResources.xaml";
            }
            else
            {
                uriSkin = @"Skins\Black\BlackResources.xaml";
            }
            _bIsBlackSkin = !_bIsBlackSkin;

            rd.MergedDictionaries.Add(Application.LoadComponent(new Uri(uriSkin, UriKind.Relative)) as ResourceDictionary);
            Application.Current.Resources = rd;
        }
    }

UI.xaml

<Window xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
    xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
    Title="Window1" Height="300" Width="300"
    Background="{DynamicResource MainBackgroundBrush}">
    <Grid>
        <Button x:Name="ToggleSkin" Content="Toggle Skin" Margin="30,30,30,30" />
    </Grid>
</Window>