Default.html.js contains the method call that initializes the Silverlight plug-in on the containing HTML page (default.html). In a typical Web file model, default.html is mostly HTML but contains a DIV and Script block that calls the CreateSilverlight method from default.html.js. Generally for each Web page that contains a Silverlight plugin, you customize the parameters in CreateSilverlight so that you can at very least size the control, and specify the XAML page that loads the UI. For more info on that: http://msdn2.microsoft.com/en-us/library/bb412401.aspx
In the above link, what's refered to as CreateSilverlight.js is basically the same file as Default.html.js in the samples, and is also basically the same file as TestPage.html.js that comes from the 1.1 alpha tools installed Silverlight project templates for Visual Studio "Orcas". There are slight inter-related variations in projects/naming schemes/folder structures but the idea is the same: define a script method that instantiates the plug-in, in such a way that you don't need to change anything in the other JS file (Silverlight.js) and you could deploy Silverlight.js site-wide, as-is.
I don't really know how to address your specific problem with the archives of the samples. Sometimes the archive viewer (before extracting, just from doubleclick of .ZIP) is funny about how it acts with file extensions of the in-archive files, and a lot of that will depend on your unique system configuration, so I might not be seeing what you see. I'd recommend just Extract All and view the expanded archive, which gets the files out of the viewer and into the "real" file system. Sorry if that's what you're already doing, it isn't clear from your question.