<p>I'm wondering if there are any architectural frameworks out there to create desktop or standalone applications, in Java or C# for instance. It seems that there are tons of them available for web applications but I can't find many good resources on frameworks or architectural best-practices for desktop development.</p>

<p>Ideally I would like to know if there is any source code available of desktop applications that would be considered to have a good architecture or are built with a certain framework.</p>

You can use some of the same approaches in client development that you use in web development, such as Model View Presenter. The System.Windows.Forms namespace has everything you need to build a client application in C#, with the rest of the .NET Framework available to provide the services you need (such as IO and remoting).
As far as source code for solid architectures in desktop apps, look at the code for
Paint.NET
and
SharpDevelop
. Both have very different approaches that will be interesting to you.
Sorry for the .NET slant of this reply. It's what I know best. :)