The friendship that develops between Bart and the Waco Kid. The crowning moment has to be when Jim makes Bart laugh after his encounter with a Racist Grandma.
Said Racist Grandma bakes a pie for Bart in gratitude later in the film. Even though she tells Bart not to tell anyone about it, Bart doesn't mind and appreciates the thought.
The expression on the face of Bart's friend on the railroad as he rides up to the railroad worksite, combined with a slow version of the movie's theme song, was really a warming scene. The sheer and unabashed joy of two friends reuniting when they never thought they could (due to one going off to be hanged) is always heartwarming.
The scene in which the townsfolk agree to give the railroad workers some land to homestead in exchange for their help:
Olsen Johnson: All right, we'll give some land to the niggers and the chinks...but we don't want the Irish!
Bart: (assess the railroad workers reaction) ...No deal.