I ride public transportation practically every day and totally understand the problem Travalert is trying to solve. You will be on a subway, train, or bus tuning out to music or even grabbing some shuteye and you almost miss your stop and your heart jumps in your chest. I usually set a alarm on my BlackBerry when I am listening to music but with train and bus times ranging based on signal issues or traffic it gets a bit tricky.
Travalert offers a quasi solution with their $1.99 BlackBerry app. They let you set a GPS alarm when you are a specified distance from your stop or simply set a timer for when you are a specified amount of time from your stop. You can select between sound, vibration, or even song alerts and you can save an alert to use again next time. I am not sure how the GPS alert would work in the underground NYC subway but other transportation systems like the above ground trains should work.
The only problem with Travalert is that is currently has two flaws. First of all the app is only available for the BlackBerry Bold 9650 and Bold 9700 for some odd reason (US and Canada only). They have also managed to make the app over 4MB which is pretty crazy.