The concept of Homer accusing Peter of his beer from his show, Pawtucket Patriot Ale, ripping off Duff Beer, the beer from his show, was a reference to how many people have accused Family Guy of ripping off The Simpsons.
In one scene from the trailer, Peter and Homer are seen jumping over the Springfield Gorge. Peter shouts "We're gonna make it" to which Homer retorts "Trust me, we're not". This references Homer jumping the gorge in "Bart the Daredevil" and Homer and Bart's near-failed jump over the same gorge in The Simpsons Movie.
When Peter and Homer are done fighting and walk away, Comic Book Guy show up and say that's the worst chicken fight ever, which is a running gag in Family Guy when Peter fights Ernie the Chicken.
During the fight scene, Homer attacks Peter by throwing Emmy Award Trophies at him, which makes Peter reply "Hey, That's no fair, I don't got none of them!!" a jab at Family Guy never winning Emmys.
At the end of the episode, Stewie says that Bart sounds like a girl, referencing that he is voiced by Nancy Cartwright, who is in fact, a girl.
Bart tells Stewie that Nelson has been bullying him for 24 years, referencing to how long The Simpsons has been on TV then.
After the fight, Peter tells Homer, "I just wanted to make you laugh and cry. I'm a Family Guy." This is a take on the lyrics from the Family Guy theme song.
While entering the courthouse, Peter says that he's tired because they "usually do this things for half a hour", a reference about this episode having one hour of duration, the double length of a normal Family Guy episode.
In a cutaway gag scene, it shows Bob Belcher from Bob's Burgers in the plane with Homer and Peter. Peter says that they have to carry him because he can't do well on his own, referencing to the fact that Family Guy is the only reason people watch Bob's Burgers.
Cleveland Brown from The Cleveland show was then seen in a crashing plane, referencing to how when Family Guy let Cleveland go to make his own spin-off series, the show was cancelled after only 4 seasons.
The aliens Kang and Kodos from the Treehouse of Horror series (and various episodes outside the THOH series) appear along with Roger, the alien from 'American Dad!'.
Harry Shearer was reportedly unavailable for this episode, so his characters have no dialogue, except for Lenny Leonard, who's two lines, a sigh and not so much, was proved by Seth Green.
The chalkboard gag stating "Spoiler alert: Unfortunately, my dad doesn't die" during the opening of The Simpsons'Season 26 premiere "Clown in the Dumps" is a reference to Homer getting crushed by Kodos and Kang's spaceship.
It is unknown where all the blood came from when Homer was lying unconsious under the spaceship after it fell on him when the fight was coming to an end. Additionally, it is never explained how he survived being squashed so gruesomely and getting back up seeming like nothing happened at all. Usually, when a character is crushed gruesomely on both The Simpsons and Family Guy, they either die or get fixed at the hospital.
Stewie uses Bart's catchphrase "Eat My Shorts!" to Nelson forcing him to eat his shorts while torturing him.
Bart tells Stewie that Nelson picked on him for 24 years which is hinting that this crossover takes place between seasons 24 and 25.
Seth MacFarlane and Matt Groening were seen in the very back of the courtroom in the courtroom scene.