A Long Island Railroad route from Atlantic Terminal in Brooklyn to Jamaica in Queens is in development by Kevin (ipac).
The (D) extension to Coney Island-Stillwell Av as well as the (B) and (Q) extensions along the Brighton line are in development by JayJay85. As far as I know, the (2)'s northbound extension is not in active development, nor are any routes for Metro-North, the Staten Island Railway or Amtrak.