The “Bolivian tree lizard” is a fictional species. However, its behavior mirrors the habits of birds which are brood parasitic, such as the cuckoo and cowbirds. Its impact on birds may also be a reference to the brown tree snake and its impact on Guam's native birds.
This episode was actually a B-story that had been unused for a long time due to having no place in the plot. The original story, however, focused on Homer finding a bird's nest in one of the nuclear plant towers and trying to find a home for the birds before the winter comes.
This is the final appearance of Troy McClure and the final appearance of Phil Hartman in The Simpsons as he was murdered by his wife (who then committed suicide) on May 28, 1998, roughly four months before the episode aired.
"The Good Son" is referenced in the scene with Nelson and Bart shooting the birds. The red scarf Nelson is wearing resembles the very scarf Henry Evans (Macaulay Culkin) is wearing in the movie.
Nelson was humming the theme song of The Simpsons as he was cooking a carrot.
Technically speaking, the snakes and gorillas wouldn't have been necessary. Since the ones that Bart hatched were related, the rest of the lizards were inbred. As a result, they wouldn't have lasted very long. Therefore they are never seen again for the rest of the series.