Are you using Context.RewritePath and having problems with Themes?
Well I sure was. I was rewriting paths in a sub folder to a single template page in the root of the site. This really monkeyed up all the paths to the App_Themes folder. None of the images or css links worked anymore. Then I found that ASP.NET 2.0 added an overload to RewritePath that takes a second param to tell it whether or not to change the virtual path. Setting this to false fixed everything!
Check it out here: http://msdn.microsoft.com/en-us/1kz7fdx9.aspx