I've been involved with a number of early-stage businesses, most recently as CTO of WinePicks. I've been sharing my thoughts on business, law and technology here for almost 8 years. Want to know more?
MTA's new Trip Planner
about 4 years ago 
MTA recently launched a new service called Trip Planner. I've used it a few times since I'm still learning some of the buses and trains around our new offices, and it seems to work pretty well.
What I like about it more than HopStop is that it gives you multiple routes and is actually tied into the schedule. After all, something may be 30 minutes of travel time, but if you're waiting on a bus that comes every 25 minutes or something, the real cost of the trip is longer.
Of course, as Dan points out, it would be better if they actually tied into the service advisories, but like he said - maybe next version.
