The title is also a reference to the film Brother from Another Planet.
When Bart covers Cecil's eyes and asks "Guess who?", Cecil guesses "Maris". Maris was Niles' unseen wife in Frasier.
In an ad for the episode, Sideshow Bob while slamming his fist on the table angrily tells Cecil "Mother had high hopes of us becoming prominent psychologists, you know!", a reference to how Bob and Cecil's respective actors' characters in Frasier were both psychiatrists. On a similar note, this marked the first mention of Dame Judith Terwilliger.
After Lisa realizes Bart lied about going to Dairy Queen, Bart then promises Lisa they will go on a water slide. Bart ends up coincidentally keeping his promise when he, Lisa, and Sideshow Bob slide down one of the conduits in the dam.
When the crowd boos after Mayor Quimby defends the choice to release Bob, Ruth Powers has red hair instead of her usual brown hair.
Bart was aware about Bob trying to murder him, but he already understood it in Cape Feare.
When Bart is praying, his Krusty poster depicts Krusty's face and beard colored yellow instead of white and tan respectively.
Bart calls Bob an unstoppable killing machine even though Bart and Lisa have Stopped him every time he has tried to kill anyone(which Bob alludes to while having dinner with Mrs. Krabappel).
While Sideshow Bob holds Lisa back, a piece of his blue shirt above his hand briefly turns red like his tie.
As Bart block's Cecil's eyesight, a piece of Cecil's hair is briefly colored yellow, making him look partially bald.