You can get the lat/lon coords of all the stations using the MassGIS data. They even have the Silver Line in there. There are the coords for the stops, as well as the coords that make up the routes.
(from another post on the subject). Turns out, it’s fairly easy to convert the MassGIS data (get it here: http://www.mass.gov/mgis/mbta.htm ) using Linux. You can use the GDAL library tools to convert the ERSI shape file to GML in the WGS84 Datum (lat/lon embedded in friendly XML).
In Debian, I did:
sudo apt-get install gdal-bin mkdir mbta/ cd mbta unzip mbta_shp.exe ogr2ogr -t_srs WGS84 -f GML MBTA_NODE.gml MBTA_NODE.shp
and voila! With a little code, that can be imported - complete with placenames.
(copied from my comments at MojoDNA.)
http://mojodna.net/2005/04/21/ongoing-mbta-work/#comment-53