I have yet to see a forward-thinking and possibly pie-in-the-sky rail plan for the United States that I didn't feel like posting here, and this plan from America 2050 is no exception. They have a passenger rail plan map which includes megaregions, which points up the usefulness of rail in integrating the country's magalopoli:
They also have a plan for a freight network:
You can read their policy brief here (pdf), though it's pretty much your standard pro-rail boilerplate. Which is to say: I heartily endorse it!