Number One with a Bullet: The 5 Best Speeding Trains in Cinema
Money Train
This exists. I hadn't given Money Train a second thought since seeing it, but watching the clip below made me realize not just what a bad movie it was, but how the special effects involved were really not terrible. I'll believe that a subway train could somersault like that; I won't believe that Wesley Snipes and Woody Harrelson could jump from said subway train, however.

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.