See intro blogpost here.

When applying default theme and template to custom controls that you declared in "/Themes/Generic.xaml" it's done differently in Silverlight and WPF:

public class MyControl : Control
{
    public MyControl()
    {
#if SILVERLIGHT
        this.DefaultStyleKey = typeof(MyControl);
#endif
    }
    static MyControl() {
#if !SILVERLIGHT 
        DefaultStyleKeyProperty.OverrideMetadata(
            typeof(HoverControl),
            new FrameworkPropertyMetadata(
            typeof(HoverControl))); 
#endif
    }
}

Also, in the WPF Assembly, you need to register the theme file in AssemblyInfo.cs This is done with the following line of code:

[assembly: ThemeInfo(ResourceDictionaryLocation.None,ResourceDictionaryLocation.SourceAssembly)]

Next: WPF vs. Silverlight - Part 2 - XamlReader