The Simpson family looking for the body is a reference to the film Stand By Me.
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 The 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 lie about how Mr. Smithers, Sr. died. Mr. Burns says that he told Mr. Smithers, Jr. that his father was killed by women in the Amazon, and says that it had no effect on him. Then, Waylon uncontently and hesitantly agrees.
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. It is possible the "Waylon Smithers, Sr. dying" scenes with a baby Waylon Smithers, Jr. take place several years before the "Homer finding the body" scene, though this is most likely just an oversight by the producers/screenwriters, as this show places little emphasis on overall continuity and consistency.
When young Moe shoots Fat Tony, it was clear that he has acne. However, when Fat Tony and his gang runs for their lives, Moe's acne is no where in sight.
Wasn't Moe's hair a "chestnut" color in other episodes, when he's childhood was seen, instead of black (Or he could possibly had his hair dyed).
Fat Tony and his group is a lot older than Homer, shouldn't he been in his 20s at the time in the flashback? It is never revealed exactly how old they are.
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.
The reason Lisa cut him off so quickly, was because writers didn't want people to switch off because they'd think it would be another clip show.