When Bart and Lisa fell into the hole to rescue Milhouse, It's possible to see a skeleton with Fred Flintstone's clothes in a "car", similar to the one in The Flintstones series, a reference to the series taking place at Stone Age.
This segment parodies the movie Chronicle.
When Milhouse summons the stone faces out of the ground, It may be a reference to the Manga and Anime Fairy Tail (Tartaros Arc).
The plot line of "Wanted: Dead, Then Alive" happens to be similar to that from the The Itchy & Scratchy Show's episode The Tears of a Clone, where following Scratchy's funeral, Itchy plans to regain his satisfaction by reanimating multiple versions of Scratchy and murdering them over and over again. Similarly in the former, Bob consistently brings Bart back to life only to keep on killing him.
The mask that Bart wore also in the opening theme seemed much like/was Huckleberry Hound reference.
In the opening theme the gravestone of the "monster" was written Frank Grimes.
In Wanted Dead, Then Alive, Homer shouts at Sideshow Bob "That's for trying to frame Krusty!" A callback when Bart got Bob arrested for framing Krusty for robbery in Krusty Gets Busted, which is the very reason Bob has been trying to kill Bart in the first place.
"Wanted: Dead then Alive" is one the few Treehouse of Horror stories that, story-wise, isn't a parody or based on something in pop culture as it is centered around the idea of Bob successfully forfeiting his goal in murdering Bart.
This is the second episode where Bart and Lisa get superpowers from radiation. The first was Treehouse of Horror X.
This is the second Treehouse of Horror where Bart and Lisa have special powers, but Lisa is much more powerful than Bart because of her intelligence. The first time was in Treehouse of Horror XII.
The Gracie Films logo didn't have the scream, instead it was replaced by Homerzilla roaring.
This is the second episode to be rated TV-14 for Season 27.
This episode also marks exactly 25 years since the first Treehouse of Horror which aired on October 25, 1990.
One of the prerelease images for Telepaths of Glory has Lisa playing various instruments with her powers while Homer and Bart watch her. But in the final version, Bart is not present and Homer interrupts her, saying that "The musicians union does not allow this!", which makes her drop all the instruments.
This is the only Sideshow Bob episode to be non-canon and a Treehouse of Horror episode.
Wanted: Dead, Then Alive
After Bob tried the reanimator machine for the first time, there's a skull with two wires connected to it's eye holes on the background. After the second test, however, the skull and the wires disappear.
Sideshow Bob stated that he has tried to kill Bart for 24 years when it should really be 22, since Cape Feare, the first episode where he tried to kill Bart, aired 22 years earlier.
During the montage, the word "Reanimate" on the machine only appears when Bob pulls the lever, but it is shown with the lever on the normal position when the family rescues Bart.
It is unlikely that the fish were getting fat and ugly because of the donuts, as Homerzilla was eating all of them.
Telepaths of Glory
Milhouse killed Dolph by throwing him in a volcano, but he reappears at the "whack-a-mole" game with the bullies.
Milhouse likely escaped the volcano.
The Comcast description says radiation exposure gives Lisa, Bart and Milhouse superpowers despite Bart briefly getting superpowers for a short time only before losing his superpowers a few seconds later (due to his brain not being powerful enough).