http://wpfwonderland.wordpress.com/2007/08/11/mixing-external-mergeddictionaries-with-local-resources-in-appxaml/
Adding local application resources
Even though it is easy to add external resources it’s likely that you’ll want to have a style or other resource that you don’t intend to shared across applications. You could isolated these resources within a single page (Page.Resources) or element (DockPanel.Resources) But what if you want to add them to <Application.Resources> tag? You can do it as long as you know the correct location. They have to go between the </ResourceDictionary.MergedDictionaries> and </ResourceDictionary> tags.
<Application.Resources>
<ResourceDictionary>
<ResourceDictionary.MergedDictionaries>
<ResourceDictionary Source="WorkshopHelpers/MainResources.xaml"/>
</ResourceDictionary.MergedDictionaries>
<!-- Place here...-->
<Style TargetType="Rectangle" >
<Setter Property="Width" Value="100"/>
<Setter Property="Height" Value="80"/>
</Style>
</ResourceDictionary>
</Application.Resources>
</Application>
-Walt Ritscher