"Head home to see your family." Six words every player has waited to see since popping the disk in the machine.
The stranger mission "Who are You to Judge?" Though the ending is... odd, Jeb did get his sweetheart back, and for a horse, she seems to love him too. Particularly when compared with the other stranger missions, which tend to end in Nightmare Fuel or a Tear Jerker, this one is a welcome break. Then again, it says something about a game when one of the happiest endings you get is a guy being able to bang his horse.
Landon Ricketts getting to pass away peacefully in his sleep. Anyone with a solid grasp of history knows that most historical gunslinging legends (Wild Bill Hickock, Billy the Kid, ect.) were usually brutally murdered. This includes John, who gets gunned down by an entire company of U.S. soldiers even after going through hell to see his family one more time. That Ricketts was able to avoid the fate of many other legends is Heartwarming, if rather bitterly.
John Marston will also turn down propositions from hookers by referring to his mother not approving. John Marston Jr that is, AKA Jack Marston, and both his parents are dead.
If you have your horse hitched up and walk away from them but remain close enough for them not to despawn (remain in town) they will sometimes somehow unhitch themselves to find and be near you.
In Armadillo, a sweet old nun all the way from Las Hermanas may offer John a blessed cross.
Sometimes you can see people playing fetch with her dog.
Learning in the epilogue that Bonnie MacFarlane is now apparently Happily Married. Considering all the crap that happened to her over the course of the game, it's nice to find out that she was able to move on from her crush on John Marston and find someone for herself, especially since she didn't have many suitors who wanted to marry a Christmas Cake.
Uncle. For all his faults, he cares about the Marstons enough to give his life, fighting to protect them. Also, the fact that John Marston, who has no issues looting anyone, or skinning anything else, that has died, won't even loot his corpse.