The Simpson family looking for the body is a reference to the film Stand By Me, which is based on Stephen King's novella The Body.
At The Pimento Grove, there are pictures showing characters and guest stars including Birch Barlow, Barry White, Bette Midler, Brooke Shields, Stephen Hawking, Rainier Wolfcastle, Johnny Carson, David Crosby, Leonard Nimoy, Anthony and Flea from Red Hot Chili Peppers, Ron Howard, Paul McCartney, Betty White and Bumblebee Man.
In this episode, it hints that Waylon Smithers, Jr. became gay after Mr. Burns give false information about how Mr. Smithers Sr. passed away. Burns says that he told Mr. Smithers, Jr. that his father was killed by women in the Amazon rain forest, and says that it didn't have effect on him. Then, Waylon uncontently and hesitantly agrees.
Homer recalls the time he attempted to jump the Springfield Gorge in Bart the Daredevil by showing a flashback but is interrupted by Lisa before he can finish.
It reveals that Smithers' first word as a baby was "Sir", which he usually calls Mr. Burns.
At the end of the episode, Homer is placing Smithers Sr.'s skull in a memories box on the coffee table. Moe arrives, and when he sits down, the memories box is gone. After a close-up of Moe's face, the table is gone.
In this episode, Waylon Smithers, Jr. was an infant and Homer Simpson is almost a teenager, yet in Bye Bye Nerdie, Smithers was around Homer's age when Homer reminisced about his "bully problem" in grade school. The body may have been there for a number of years by the time Homer found it.
When young Moe shoots Fat Tony, it was clear that he has acne. However, when Fat Tony and his gang run for their lives, Moe's acne is nowhere in sight.
He may have gotten rid of it.
When Homer first discovers the body of Smithers Sr., the body had glasses and hair but when its face is shown, the body has no glasses or hair.
When Homer explains how he almost made it across Springfield Gorge, Lisa informs him that everyone is tired at the memory, a reference to its repeated showings in other episodes before.