S (New York City Subway service)
- Franklin Avenue Shuttle (internally referred to as the S)
- 42nd Street Shuttle (also called the Grand Central/Times Square Shuttle) (internally referred to as the 0)
- Rockaway Park Shuttle (also called Rockaway Shuttle) (internally referred to as the H)
The following services run as shuttles during off hours but retain their regular service designations:
- 5 late nights (Dyre Avenue Shuttle), originally SS
- A late nights (Lefferts Boulevard Shuttle); in addition to regular A service
- M weekends and late nights (Myrtle Avenue Shuttle), originally SS
- R late nights (Bay Ridge Shuttle)
Former uses 
Other routes have in the past been designated S; the label has also been used for temporary shuttles due to construction. Before 1985, all shuttles had the label SS and S was reserved for "special"' services, including IND trains to Aqueduct Racetrack. The SS label was first applied in 1967, when all services were labeled due to the completion of the Chrystie Street Connection.
Former uses of the S or SS designation are as follows:
- Bowling Green – South Ferry Shuttle (1909–1977)
- Culver Shuttle (1954–1975)
- 63rd Street Shuttle (1998–1999)
- Grand Street Shuttle (2001–2004)
Some shuttle routes also used the H or HH designation, which were the last to be assigned to the Independent Subway System. Former uses include the Court Street Shuttle from 1936 to 1946 and Rockaway Park Shuttle until 1993, when that route's label was changed to a blue S. A temporary shuttle opened in November 2012 after Hurricane Sandy destroyed track connecting the Rockaways to the rest of the system used the H designation.
When the Transit Authority began assigning labels to all services, the Third Avenue Elevated was designated as 8 because it was deemed too long to be considered a "shuttle". However, trains on this line showed SHUTTLE on their rollsigns instead of "8". The service was discontinued in 1973.
Lenox Terminal Shuttle (1905?–ca. 1970) 
The Lenox Terminal Shuttle (also Lenox Shuttle and Lenox Avenue Shuttle) ran between 148th Street and 135th Street when the 3 did not run. Prior to May 13, 1968, it was called the 145th Street Shuttle, running only to 145th Street, and only from 21:00 to 01:00. It was in place by 1918, but may have been started in 1905 when the IRT White Plains Road Line opened to the IRT Lenox Avenue Line.
Between 1969 and 1972, it was folded into the 3, but continued to run as a shuttle at those times. Late night 3 service ended on September 10, 1995 and was not restored until July 27, 2008. During the time, the route was served by a free overnight shuttle bus.
Myrtle Avenue Shuttle (1969 – 1973) 
After the BMT Myrtle Avenue Line south of Myrtle Avenue ceased operation on October 3, 1969, the MJ service was discontinued and the current nighttime/weekend M shuttle was formed. However, this service was labeled SS and considered a separate route from the M until the two routes merged in 1973.
Nassau Street Shuttle (1999) 
This shuttle ran only from May to September 1999 during the rehabilitation of the Williamsburg Bridge. The shuttle ran from 06:00 to 22:00 daily from Essex Street to Broad Street (Chambers Street on weekends). At Essex Street, the B39 bus provided service across the bridge to Marcy Avenue, where customers could transfer to the M, which connected to the J at Myrtle Avenue.
Further reading 
- "One Dies in Wreck of Subway Train," The New York Times, December 9, 1918, p. 13
- "Coming Transit Reductions: What They Mean for You," The New York Times, August 20, 1995, p. CY10
- "A Subway Station is Shuttered, the First in 33 Years," The New York Times, September 11, 1995 (the article is about Dean Street on the Franklin Avenue Shuttle, and the headline refers to the 1962 closing of Worth Street; several old-style elevated railways were closed since then, as well as the Culver Shuttle which hosted both elevated and subway service at one time)
- Line By Line History