I know VS2008 has the remove and sort function for cleaning up using directives, as does Resharper. Apart from your code being \"clean\" and removing the problem of referenc
There is one compile-time difference: when you remove a reference, but still have a using directive in your code, then you get a compiler error. So having a clean list of using directives makes it a little bit easier to remove unused references.
Usually the compiler removes unused references, but I don't know if that works when a using is in the code.