Number One with a Bullet: The 5 Best Speeding Trains in Cinema
The Taking of Pelham One Two Three
Not the Tony Scott-directed remake (what is it with this guy and trains?), but the dusty old original, co-starring Walter Matthau, Robert Shaw and a cast of real local-looking New Yorkers. There is something both corny and legitimate in the way the straphangers are presented during the finale's runaway train montage: They're full-on panicking, but still New Yorkers. It might seem forced, but the gallows humor and shrug-it-off mentality is probably closer to reality than anything else. (Things get really fun at around 3:10.)

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.