I am playing Just Cause right now and I just did a mission with a train and tank fuel.
Did I list Saints Row? If not then here it is.
Mafia 1 and 2 seem to have some form of train in them.
Spoilers if you haven't played or completed HL 2 - episode 2
I bet I'm repeating myself or someone but Half life 2 you begin on a train, go through a mine, go through a train yard, crawl through train wrecks, and have to cross an train bridge which seems to be falling down.
Episode 1 seems to like derailing. The first train you get one derails. then there is the whole ending which is centered around trains.
Episode 2 starts in a train wreck then you go into a mine. After the mine you won't see trains until after when you get the car and then they are static objects which are meant to show off your driving skills it seems.
Some trucking arcade game I once played had you deliver a diesel loco on a flat bed to somewhere.
If you are easily scared, do not play Crystal Skull
Lol I found that out to late and boy did it freak me out. To bad I Have to complete it since I'm dedicated like that. And not to mention since the mention of the snake in the game... I am afraid of snakes. I avoid them everywhere from pictures to the reptile house.