Tips for setting up a public transportation route planner

Public Transportation in Metropolitan Areas you can use the google maps api

How to get Google Maps Public Transit Directions by HTTP server-side request

There's a defacto standard way to encode and interchange transit data. Lots of transit agencies are releasing their data in Google Transit Feed Spec format. You might check to see if your agency has already done so. There are also open source tools for dealing with GTFS. For instance: http://code.google.com/p/googletransitdatafeed/