The pilot of the ship, Michael, is a reference to Michael Knight, the protagonist in Knight Rider.
Homer mentions Star Trek when he is setting the scene for the story of Maggie's pictures.
Homer's version of the story has the style of the 1988 action film Die Hard, and includes him hearing a man who sounded like Hans Gruber, the main antagonist, announcing that the Springfield Nuclear Power Plant has been taken over by terrorists.
The kid, the orphan-looking kid in Barney's Bowlarama who wants to go to California, is a reference to the 1989 film The Wizard where the protagonist kid Jimmy "The Wizard" Woods suffers from PTSD and keeps repeating the word "California".
Patty calls Aaron A. Aaronson to tell him about Marge's pregnancy. Aaronson was mentioned by Lisa in "Sideshow Bob Roberts" when she went through the election results.
When Homer finds out that Marge is pregnant with Lisa, he runs up the stairs, but on the wall you can see a picture of Lisa (or at least someone who looks like her). There is also a picture of Maggie on the wall before Maggie was born.
Also, when Homer finds out about Lisa, he was upstairs in the bathroom with Bart when Bart was flushing the keys down the toilet, in "Lisa's First Word".
Ruth Powers is at Marge's baby shower despite it being set long before Ruth knew Marge.
When Homer and Marge went into their room after the trip to the beach, the bathroom door is suddenly the hallway door, and the next scene in their room is the bathroom again.
Dick Clark's birthday on the calendar falls on the 16th, even though he was born on November 30, 1929.
In the scene where Homer finds out Marge is pregnant with Lisa, Marge and Homer appear to be sitting in their current house despite the fact that in "Lisa's First Word"; we see that the family doesn't move into their current house until after Homer already knew Marge was pregnant.