City Hall Loop was one of the original IRT stations. (Not IND as stated in another answer.) The station's tracks are still used to turn the 6 train around. Passengers can now stay on the 6 train as it turns through the City Hall Loop to see the restored station from the train.
Worth Street. 18th Street, and 91st Street was made redundant when the MTA lengthened the platforms at the adjacent stations.
South Ferry Station was closed, but underwent major reconstruction to lengthen its platform starting in 2005, but was flooded during Hurricane Sandy and requires major repairs.
This leaves the 145th Street as the only station where the platform is not long enough to accommodate the full train. Just south of the station are the switches to the tunnel to the Bronx, and just north are the switches for the 148th Street Terminal and Lenox Yard.
Here is the link to the list and photos of all closed subway stations in the system:
http://www.nycsubway.org/wiki/Abandoned_and_Disused_Stations
This is actually a great site, I am really glad I found it. It has everything you wanted to know (and some things you didn't even know you wanted to know) about NYC Subway, its history, rolling stock, stations, and structures.