A local roaster with three locations in Flagstaff, Late for the Train is one of the oldest and most successful coffee shops in town. The downtown location is the oldest and largest; stop in on the first Friday of the month to find work from local artists on display, and maybe catch a local band. The coffee drinks have strangely quirky names and descriptions for fairly standard drink offerings, but the quality is excellent. They offer a couple of unusual spicy drinks, like hot cocoa spiced with chili and almonds, and seasonal espresso beans.
One location is on the way out of town to the northwest (toward the Grand Canyon); it's a perfect stop before hitting the canyon or after a long day of skiing. The last is at the Flagstaff medical center, a bit out of the way for a casual stop.