When Homer shouts the F word, it is censored by a church organ playing an F minor chord.
Mr. Burns collapses on a sundial pointing his arms at S and W - which to his eyes look like M and S - identifying the initials of the shooter. This resulted in several characters having their names permanently expanded solely for the sake of red herrings: Seymour Skinner's name was revealed as W. Seymour Skinner - this is written on a diploma behind his head in one scene - while Moe the Bartender became Moe Szyslak, and Sideshow Mel's real name was revealed as Melvin van Horn, presumably to eliminate him, though it could still have been interpreted as not MS, but SM, Sideshow Mel.
Back when this episode first aired, there was a big contest over the summer to see who could guess the shooter.
As Mr. Burns collapses on the sundial, it is seen that the gun he was previously carrying has gone missing. This was inserted as an intentional freeze frame clue to show that he had been shot with his own gun - but it would also mean that regardless of the weapon a character might be seen with, they could still have shot him.
The idea for the episode came from Matt Groening, who had wanted to do an episode in which Mr. Burns was shot, which could be used as a publicity stunt.