Henry Fonda shoots a little kid, that's probably the biggest reason it got an R.
Re classic westerns from that period, Wikipedia says that the full cut of The Wild Bunch got an NC-17 in 1993 but they got them to change the rating without recutting it. I'm fairly certain that none of the additional material is violent, it's just more character development. So they were trying to give an NC-17 rating to something that had been rated-R in the 60s. I wouldn't be surprised if that was the argument that got them to change it back.
> The Godfather Part III almost got it? That'd be hilarious!
That's really weird but of course they were always going to cut it for re-rating.
> The "Director's Cut," presumably added back in the graphic violence from the original cut but was mostly made up of 9 minutes of additional footage. Shots from the scene in question can be viewed in the making of Documentary "The Godfather Family," which discuss the scene in question of a man being stabbed in the neck with his glasses, and the dramatic spray of blood that followed.
I remember that scene from the original cut. I guess now we can watch the x-rated Godfather III!
Man Bites Dog is another one I've seen.