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 is happy enough that she's kind enough to do that much.
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 succeeds at the incredible task of being both incredibly sweet and hilariously wrong.
"Nowhere special. I always wanted to go there." Especially after that line showed up a lot after Gene Wilder's passing.
The fact that over the course of the film the people of Rock Ridge go from wanting to gun down Bart in the street as soon as he rides into town to begging him to stay at the end. "He conquered fear and he conquered hate" indeed.