Here's an example of how I organize my solutions, which mirrors the namespace structure.
The project has a default namespace which, in this case, is CompanyName.ProjectName
Source files are organized logically into a directory structure. In the example, my WF4 activity designers are organized under Activities in a folder called Designers.
The way VS works is that, as you create directories in a project, you are also creating namespaces. So, if I were to add a new activity designer called "Foo" in the shown directory, its namespace would be
"CompanyName.ProjectName.Activities.Designers"
Visual studio takes the default namespace, then uses the folder structure to determine the namespace for a particular file. Of course, once the file is created, and you move a file, it isn't automatically refactored. But the system works very well for not only controlling namespaces for classes, but also for keeping files organized.