Question: I want my WPF application to be skinnable, by applying a certain XAML template, and the changes to be application wide, even for dynamic controls or controls that aren't even in the visual/logical tree. 

What can I use to accomplish this type of functionality? Are there any good resources or tutorials that show how this specific task can be done?

Answer: 
The basic approach to take is using resources all through your application and dynamically replacing the resources at runtime. 

See <http://www.nablasoft.com/alkampfer/index.php/2008/05/22/simple-skinnable-and-theme-management-in-wpf-user-interface/> for the basic approach
The replacing of resource will work but I found "structural skinning" to be more powerfull! Read more about it on CodeProject...

<http://www.codeproject.com/KB/WPF/podder1.aspx>