Even the savviest New Yorker needs a subway map or bus schedule at some point, so go download NYCMate, a free app for Android and iPhone that packs cached, pinchy-to-zoomy maps and schedules for NY public transit. [iTunes, Android; NYCMate]
I've used CityTransit since the apps started rolling out on the iPhone, but I've been a little miffed in the last two weeks as they haven't updated their app for iOS4 - it still works but the formally sharp and crispy map is now pixelated, and difficult to read when you attempt a zoom-in (not just a result of the new "Retina Display" revealing pixels).
This NYCMate app is insanely sharp. The type is so nice. I will miss the way CityTransit can use LocationServices to show you the nearest subway station on Google maps, service updates, as well as how it shows you a list of all the stops a line makes, but I will try this for a while.
Also, I'm starting to lean towards buying that ExitStrategy app - the one that shows you where on the train or platform you should be to be closest to your exit or transfer:
One of these apps just needs to combine all of the features of the others and be done with it.