Here are my contributions...
Well, StarFox 64, the best game ever, had a train level. You were in a tank, and you had to blow up all of the cars on it, then, you could throw a switch, and send it into a fuel bunker.
Another N64 favorite, Star Wars: Shadows of the Empire had a train level as well.
That new Wii Rampage game has two:
In Chicago, there's a typical L train, and in New York City, there's a CSX train, complete with Rail Box TTX cars, although instead of CSX, the little AC44W reads "OIX". Otherwise, the paint schemes are the same as their real-life counterparts.
The older Rampage games had them as well, but they never resembled an actual railroad.
I used to have some sort of fighter jet game for Gamcube (I forget the name), and I remember at one point in a training level, there was a short freight, but I don't remember anything else.
Rogue Squadron for N64 had a few trains as well.