Very nice article ... well done.

My only comment is about the presentation and not the content, and is only meant as a suggestion to improve the readability.   The source code snippets are a little hard to read with the color combinations and the background highlighting.  I would suggest looking at something like http://manoli.net/csharpformat/format.aspx, which is a great web site for formatting source code, whether it's c#, vb,html or xml.

You just paste your code, hit a button and then copy the results to your web page, blog or module. 

If you are using LiveWriter, there are some great source code formatter plug ins.

So, using the http://manoli.net/csharpformat/format.aspx web site, your source code snippets could look like this .. which is much easier to read.

   1:  using DotNetNuke.Security.Permissions;

   2:  using DotNetNuke.Entities.Modules;

   3:  using DotNetNuke.Entities.Modules.Definitions

   4:  using System.Collections;

   5:   

   6:  public string UpgradeModule(string Version)

   7:  {

   8:      if (Version == "01.00.00")

   9:     {

  10:        // Install module permissions 

  11:        InitModulePermissions();

  12:     }

  13:     return Version;

  14:  } 

regardless, excellent article and thanks for sharing with the community!