Spirit Tracks 
One of my favorites are GoldenEye, Paper Mario Thousand Years Door (playing detective in a train), Red Steel 2 and everyone that played Uncharted 2 will probably say Uncharted 2.
Iga_Bobovic said:
Spirit TracksOne of my favorites are GoldenEye, Paper Mario Thousand Years Door (playing detective in a train), Red Steel 2 and everyone that played Uncharted 2 will probably say Uncharted 2.
Nice choices, the goldeneye 64 one is a standout. In the wii version the train is a bunch of carriages sitting flat in a contruction area and you can run through them in 30 seconds.
Final Fantasy VI's Phantom Train was pretty cool. Only train I can think of aside from the Spirit Tracks one.
The train in GCN Animal Crossing was cool. 
It was sooo much better than that effing stupid lame-ass school bus in City Folk! 
Media guys, we need video
But of course.
SteelAttack said:But of course.
I haven't seen that one, I saw the one on the train in the snow.
Uncharted 2's train sequence is the best ever. No contest. Probably the best action sequence I've ever played in any game.
Choo Choo
That is a pretty badass looking train from Spirit tracks. They should make real trains like this.
I don't remember any besides PMtTYD orient express level, U2 and ST.
There was an old arcade game I used to like which you played as a cowboy in a western setting and you would kick and punch people on top of moving trains. It also had levels where you rode a horse next to a moving train and you would shoot bad guys appering at the windows etc. Can't remember its name though
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Listen to Wu-Tang and watch Kung-Fu
Doh! How could I forget about the Bad Dudes?
It took me a while to come up with one. The train from the very excellent FPS, Darkwatch:
This was on the front of it:
here is some other art from the game:
^That reminds me of the train in The Darkness.
Now including train simulators:
That Darkwatch train is great. Looks like an evil castle or machine on wheels.
I was just thinking about the train in Go Vacation and whether you could ride it or not.
I like trains in games, like old ass train journeys that take ages like in murder mystery films. Murder on the Orient Express and the like.
What are the best you have seen? I will let someone else do Paper Mario and I will go for the Crystal Bearers.
When you get on the train you have to go through this MGS Style stealth segment to get through the guards, hiding under stuff and leaping back and forth. Quite fun and the inside of the train looks lush.