Number One with a Bullet: The 5 Best Speeding Trains in Cinema
Super 8
OK, it hasn't even come out yet, but the train wreck in the trailer for Super 8 is completely bad ass. And it involves aliens. Or monsters. Or monster aliens. As Aubrey Plaza once said, "What's in dat box, J.J.?"

Comments
Mission Impossible is definitely the best. But don't forget Speed!
Also, in Tall Target, Dick Powell has to stop Abe Lincoln from getting assassinated on a train. Movie is almost as good as the title: http://www.imdb.com/title/tt0044105/
I really like the cutaways to the speeding train at the end of "The Lady Eve," as Barbara Stanwyck rattles off the names of the men she has slept with to an increasingly pale Henry Fonda. (A scene that was copied, sans train, in "Four Weddings and a Funeral.")
How can you forget Runaway Train?!?!? Jon Voight, Eric Roberts...
And it's right there in the title!
BULLET TRAIN with Sonny Chiba as the engineer. Crazy hysteria. What SPEED was a remake of. Except it's a train, not a bus.
What about Silver Streak?
ooooh. And Strangers on a Train. And Transsiberian.
I will also go with Mission: Impossible as best train sequence.