During the montage that shows the Homer clones dying, the kids are shown with some of the outfits/appearances they wore/had during the Christmas card photo montage from Holidays of Future Passed.
In the scene where the third Homer dies, Maggie is not sucking on her pacifier, and she, Bart, and Lisa are wearing similar outfits to the ones they wear in the Christmas photo four years in the future, except in different colors. Bart's suit is navy blue instead of grey, Lisa's dress is blue instead of pink and she has an shirt underneath it, and Maggie's dress, shoes, and hairbow are green instead of blue and pink, black, and pink.
In the scene where the fifth Homer dies, Lisa is wearing her goth outfit from the five years photo. She is not wearing makeup, and her hair is still yellow but the points are not straight.
In the scene where the seventh Homer dies, Bart, Lisa, and Maggie all appear as they do in the seven years photo, except their clothes are different colors: Bart's shirt is teal instead of salmon, and Lisa's shirt is blue instead of green, her leggings are white instead of black, and her shoes are pink instead of black.
When Bart is organizing his little black ebook, Eve from Wall-E is seen.
Cretaceous Park is a reference to Jurassic Park and the fact that many of the dinosaurs from the movie were from the Cretaceous time period.
Homer's robotic body at the end of the episode is a reference to C-3PO.
Maggie's husband, which was not seen in "Holidays of Future Passed", is hinted to be Gerald Samson. They are seen for a few seconds at the Gilded Truffle sharing a drink.
Maggie has a very small role in this episode. This marks the second time since "Future-Drama" in which her future self only made a quick cameo.
Zia Simpson, Lisa and Milhouse's daughter from "Holidays of Future Passed", to which this episode is a sequel to, does not appear in this episode, nor is she mentioned. She is only seen in one of the photographs in the Simpsons' living room.
Frink's quote that he wanted to clone sheep is a reference to Dolly the cloned sheep.
Bart's profile number is SABF13, the production number of this episode.
The concept of Homer dying and being "downloaded" into a new body (clone) is a similar concept to the humanoid cylons being downloaded into new bodies after death (in the reimagined Battlestar Galactica series).
The episode's closing credits is based on the closing credits of the period drama show; Mad Men
Marge mentions that she and Homer were married for 35 years, but with the episode set 30 years in the future, they should have been married for, at least, 40 years. Although they could have been separated for five years in the past.