MTA: All But Handful of Lines Returned to Service

UPDATE:
As of November 19, 2012, the only remaining gaps in NYC MTA subway line service are the R tunnel from the Manhattan Battery to Brooklyn Heights and the two elevated A train branches serving the Rockaway Peninsula.

New MTA subway service map, as of November 7, 2012.

The only service gaps remaining are the A train lines to the Rockaways, service south of Rockaway Boulevard station; the L train west of Broadway Junction, crossing under the East River, the N train in Brooklyn and the R train passage between lower Manhattan and downtown Manhattan.