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 just for the sake of red herrings: Seymour Skinner's name was revealed as M. Seymour Skinner (it's written on a diploma behind his head in one scene); Moe the Bartender became Moe Szyslak; and Sideshow Mel's name was revealed as Melvin van Horn, presumably to eliminate him (although it could have still been interpreted as not MS but SM - Sideshow Mel).
When this episode first aired, it was shown after a special called "Springfield's Most Wanted", in which all of the suspects were listed, and possible motives for killing Mr. Burns were revealed. The special was hosted by John Walsh, host of America's Most Wanted.
In Canada due to a simulcasting glitch the key moment where Mr. Burns got shot was interrupted due to a golf game running a few minutes late. Canwest Global had to re-air the episode again the following week.
This two-part episode makes two references to Dallas (1978). The entire "Who Shot Mr. Burns?" mystery was a parody of the "Who Shot J.R.?" mystery. At the beginning of this episode, Smithers has a dream in which he wakes up to find a completely healthy Mr. Burns taking a shower, and coming to the conclusion that it was all a dream, only to wake up and find that it wasn't. Dallas (1978) pulled a similar stunt, in which an entire season, including the death Bobby Ewing, was re-written as Pam's dream, with Pam awakening to find Bobby alive and well, taking a shower.