Ok I think this is a little bit old, but I'm just finding out about this site for the first time today! It's funny how I've been to a lot of sites, but haven't seen this one ...
www.hopstop.com
You just enter the start point and end point, the times of day and pick if you're taking the train(s), cab or are walking! It's pretty sweet! Damn this is so much easier than going on Google maps and going to the MTA website to see what subways are nearby and where to transfer!
+ mon