Fantastic question.  I'd love to see some best practices shown.
I've got a lot of files that I distribute, so I've set up my project into several wxs source files.
I have a top level source file which I call Product.wxs which basically contains the structure for the installation, but not the actual components.  This file has several sections:
  
    ... 
   s ...
   
    
        ...
   
   
       A bunch of these that
   
   
   
   
   
The rest of the .wix files are composed of Fragments that contain ComponentGroups which are referenced in the Feature tag in the Product.wxs.  My project contains a nice logical grouping of the files that I distribute
   
     
     ....
    
    
      
This isn't perfect, my OO spider sense tingles a bit because the fragments have to reference names in the Product.wxs file (e.g. the DirectoryRef) but I find it easier to maintain that a single large source file.
I'd love to hear comments on this, or if anyone has any good tips too!