NYMS

http://www.treehugger.com/galleries/2009/07/7-best-subways-in-the-w… http://www.treehugger.com/galleries/2009/08/worlds-best-alternative… http://www.wandawanders.com/content/view/114/81/

Google Map
Google Transit – in progress
NYC Subway – very simple map of NYC with a overlay of the train lines

Websites where you input “To” and “From” addresses and gives you train/bus directions.  Also takes into consideration whether you would rather walk more/less or transfer more/less.  Gives you a street view of your end destination sometimes.

MTA Trip Planner
HopStop