USA
-NYC Subway
-LIRR (Long Island RR)
-Metro-North
-NJ Transit
-KEWR Airport Shuttle (if you want to count it)
-Amtrak (NE Corridor & Keystone)
-Port Authority of Allegheny County (Pittsburgh)
-MBTA
-San Francisco Muni
Australia
-Sydney Trains
-Sydney light-rail network
-Sydney Ferries
-NSW Trainlink
-Melbourne tramway network
-Queensland Rail City network
-G:link (Gold Coast Light Rail)
-Metro Tasmania
-ACTION (Canberra)
-Premier Illawarra (Wollongong)
Japan
-Tokyo Subway
-Shinkansen
China/Hong Kong
-Shanghai Metro
-Shanghai Maglev
-Guangzhou Metro
-MTR East Rail Line
-Xi'an Metro/Subway (hat-tip to @Zaedin1)
-Train G90 (Xi'an-Beijing)
-Beijing Subway
-Mass Transit Railway (MTR - Hong Kong)
-Hong Kong Tramways
Coming soon...
England
-London Underground