This episode's title is a reference to the third part, And Baby Makes Three, in Hubert Selby Jr.'s cult novel Last Exit To Brooklyn.
The couch gag is a reference to the James Bond gun barrel sequence.
The kid in the Bowl-O-Rama who wants to go to California is a Little House on the Prairie reference.
At the beginning of the episode, the Simpsons are watching a show called "Knightboat: The Crime Solving Boat", a parody of the David Hasselhoff shows "Knight Rider" and Baywatch..
Homer spinning around with a bowling ball in his hand before throwing it into the air and exclaiming "I'm gonna make it after all!" is reminiscent of the opening of "The Mary Tyler Moore Show" where Mary throws her hat into the air.
The song that plays while Homer and Marge have their night of dinner and dancing is "Copacabana (The 1993 Remix)", by Barry Manilow, although it is credited as "Copacabana (At the Copa)".
This is the first episode to contain Maggie's name in the title.
Bart breaks the forth wall with the line, "You can't expect someone to sit for 30 minutes straight."
When Homer finds out that Marge is pregnant with Bart and 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).
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".
Marge says that when Homer found she was pregnant with any of the kids, he would pull of his hair and scream and run off, but that doesn't happen in "I Married Marge" and "Lisa's First Word". In "I Married Marge", Dr. Hibbert says to Homer and Marge that she is pregnant, to which Homer exclaims "D'oh!". In "Lisa's First Word", Marge tells Homer, to which Homer is happy, but Bart flushes his keys down the toilet.
The two scenes in which Homer discovers the birth of his first two kids, the background clearly shows 742 Evergreen Terrace, although they still live in the apartment at that point in "Lisa's First Word".
Ruth Powers is among the people at Marge's baby shower despite the fact that she moved to Springfield in "New Kid on the Block". She could have moved to another city after this episode and then moved back to Springfield.
When Homer and Marge come back from their night out, the door in their bedroom is on the wrong wall.
When Marge tells Homer her contractions are three minutes apart, a picture of Maggie can be seen hanging on the wall, despite not having been born yet. Current executive producer Matt Selman tweeted out the error on Twitter while watching the episode on Sept. 4, 2018.
Homer doesn't become the safety inspector of the power plant until "Homer's Odyssey". And in that episode, Maggie was already born. Yet prior to Maggie's birth, Homer begs for his job back at the power plant before she is born. That very episode, and "The Way We Was" imply that Homer worked at the plant prior to his promotion to safety inspector.
Inconsistencies between this and other "flashback" episodes and other miscellaneous goofs in the flashbacks may be the result of Homer's storytelling.
When Homer and Marge go back to their bedroom, they come in through the door which usually leads to their bedroom bathroom. Also, the purple drawers can be seen when they enter from the hallway.
In some FXX reruns, towards the end of the episode, the exterior of the hospital is seen, then it skips straight to Maggie's birth, cutting out the Quimbys and Sea Captain's babies.