The Bicycle Coalition's official map makers at Steve Spindler Cartography have done it again!
Phillymap.com pairs SEPTA, PATCO and NJ TRANSIT routes along with regional shared use paths on Google Maps. You select the only the routes you want displayed on the map.
While it does not match the trip planner on Google Transit, Phillymap.com does offer you something NJ TRANSIT and SEPTA do not, an online transit map that is easily readable.
One interesting feature is that you can select Farmer's Market Features which enables you to ride or bike to get those fresh fruits and vegetables while minimizing your carbon footprint.