I guess You mean municipalities. I think most systems runs within a single city or municipality, as New York. But Washington goes by some different municipalities, the same as BART, And I think Atlanta. PATH in NY-NJ runs within four municipalities, I think, and PATCO between Philadelphia and NJ also goes by some different municipalities.
Here is a Wikipedia list where You can find all United States systems and find out the ubication of the stations.
http://en.wikipedia.org/wiki/List_of...s_by_ridership