Here's the Globe article that talks about iPhone Apps but fails to mention their names:
State transportation officials said the decision to open up transportation schedules to computer software developers has already paid off with the creation of two iPhone applications that could help people trying to catch a train or a bus.Here are four iPhone MBTA Apps:
One app - a computer program that runs on iPhones - shows the user where the closest Massachusetts Bay Transportation Authority station is located, while another indicates when the next train or bus is coming.
A third app could be useful for people planning a trip to the Registry of Motor Vehicles. It shows users the current Registry wait times, said Colin Durrant, a spokesman for the Executive Office of Transportation.
MassTransit by Sparkfish Creative
iTransit Buddy - MBTA RAil by Blue Technology Solutions LLC
theNextTrain MBTA by theNextTrain
to a T by Wonderland Development
HopStop is free.
Google Maps on iPhone
Also, the Google Maps App on the iPhone is great at showing train schedules.