Number One with a Bullet: The 5 Best Speeding Trains in Cinema
Spider-Man 2
Speaking of New Yorkers: You have to love Sam Raimi and Spider-Man 2 for making New York look so much like Chicago during this elevated subway near-disaster. At least this is a thrilling reminder of how super-strong teenagers can always save the day.

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.