AS I understand they had planned to have working subway in Fallout 3
http://kotaku.com/turns-out-fallout-3s-trains-were-actually-equipped-to-1719572837
Weird way it works, you equip the train somehow.
It was scrapped, I know its working boat mods for Oblivion and I don't think they use this method as you can drop stuff on the deck of the boat and it moved with you.
Should be easier to do with an train as it would only drive forward or back, main issue would be accuracy as you would want to stay on the track,