Dracula is wearing Iron Man (Mark III) armor, the Werewolf looks like Harry Potter, the Mummy is dressed like Jack Sparrow, and Frankenstein's monster is dressed like SpongeBob.
The Werewolf's Harry Potter costume may be a reference to the character Remus John Lupin, a werewolf.
Lenny and Carl are dressed as The Blues Brothers Jake and Elwood Blues.
Homer is dressed as Zorro.
The first segment is a pastiche of numerous Alfred Hitchcock films. The main plot derives from Strangers on a Train, where two men plot to kill off each other's enemies, while other elements of North by Northwest, Vertigo and other Hitchcock movies are included. Hitchcock himself is shown in a brief cameo stepping out of a bus (as he did in the title sequence of North By Northwest).
The second segment is a parody of both 28 Days Later (a pandemic causes mankind to turn into zombie-like monsters) and Children of Men(a society on the brink of collapse due to chaos has one chance of survival thanks to someone with a medical anomaly [in Children of Men, it was the last woman on Earth who is able to have a baby (as all the women in the world in Children of Men suffer from infertility); in Don't Have a Cow, Mankind, it's Bart's immunity from Krusty's latest burger]).
If you look very closely you can see that the theatre reads Madea Goes To Hell.
In the opening, the bullies are wearing costumes of John 117, The Joker from The Dark Knight, and Black Suit Spider-Man from Spider-Man 3.
The first segment title is a parody of "Dial M For Murder". The second segment title is a parody of Bart Simpson's catchphrase: "Don't have a cow, man". The third segment title is a parody of "There's No Business Like Show Business".
Kodos' shushing everyone is a reference to the Gracie Films closing logo. Actually, the actual Gracie Films closing logo wasn't changed, it was did as usually in every Treehouse of Horror series. It's the same as Treehouse of Horror VIII.
In the second segment, when Bart and Homer initially step outside and Homer blows their cover, Kirk Van Houten is seen in the back right of the muncher mob breaking down the front door to try to get to the Simpsons. Yet, when they make it to the safe zone, Mr. Van Houten is clearly seen in the front of the crowd before the Simpsons push themselves through. While it may be a goof, it could also be someone similar to him, though the physical features are astonishingly alike.
Ralph Wiggum is seen as a muncher eating his own arms. Yet he is seen happy and healthy at the end of the segment. Of course this could mean that Bart's immunity also doubles as a cure for the already infected. You can see Homer is still in his "muncher cage" behaving like a muncher.
After Homer becomes a muncher the gun turns into a single barrel.