As for iPhone apps, there aren't many good ones that have the hopstop-like trip planner, although with the recent updates to the Google Maps app (Maps, native to the iphone), it can figure out which subways you need to go from A->B.

However, I've found a handy app called City Transit that has the full map, and a map for each line, as well as a link to any service changes. It does cost something, but I forgot how much.