I was just asked how to get from Staten Island to downtown Brooklyn without taking the subway. This is theoretically possible...so I looked up NYC transit maps and found HopStop.com, with fully integrated transit maps and Google Maps (including the 360 degree street view, which they offer you at transfer points...fragging brilliant, if you ask me) for Boston, Chicage, New York, San Francisco and Washington, DC into a web interface that plots door to door trips for you.
AND it has a developer API.
The New York City part is seriously useful, and when the Metro North, LIRR and New Jersey services are out of beta it ought to be seriously impressive. You might want to investigate it if you live in one of the cities it serves up.
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They must be making progress
the maps used to suck!!