The final segment references Pan's Labyrinth again: the throne room is the same, Marge and Homer resemble the King and Queen of the underworld, Lisa is dressed as protagonist Ofelia, there are small fairies flying about, and Bart resembles the Faun.
Oh, the Places You'll D'oh
This segment is a parody/tribute to the works of Dr. Seuss.
The title is a parody of his final book, Oh, the Places You'll Go!
The story is primarily a parody of The Cat in the Hat. Bart and Lisa's outfits resemble the ones that Sally and Conrad wear in the story.
The little helpers under the Fat's hat is a reference to the book's sequel, The Cat in the Hat Comes Back.
The Borax is a parody of the title character of The Lorax. The Fat in the Hat calls him a "sell-out" for plastering his face on merchandise, a reference to the controversial advertising campaign of the 2012 film adaptation of the story.
The Fat in the Hat knocks over a tower of turtles stacked on one another, a reference to Yertle the Turtle.
Ned Flanders' appearance resembles that of a Sneetch from The Sneetches.
The inanimate pair of pants is a reference to the story What Was I Scared Of?
Mr. Burns calls the Fat in the Hat a "son of a gritch", a reference to the Grinch from How the Grinch Stole Christmas!. In addition, Lisa's outfit resembles that of Cindy Lou Who.
A drunkard sleeping outside of Moe's is surrounded by hats, a reference to The 500 Hats of Bartholomew Cubbins.
A parody of Horton the Elephant from Horton Hears a Who! can be seen at Moe's drinking from a tap with his trunk.
Moe's appearance here does visually resembles The Grinch, because of their shared grouchiness.
The "three-humped Gumbamel" is a reference to the "seven-hump Wump" from One Fish, Two Fish, Red FIsh, Blue Fish.
The mask the Fat in the Hat wears when blowing up city hall looks similar to Guy Fawkes' mask from the film V for Vendetta.
The classic MGM lion roar can be heard when the Fat in the Hat frees the animals in the zoo.
Freaks, No Geeks was supposed to take place in 1932 but when Homer tells the kids his story it is in the present time. Since this is non-canon, he could have lived for 81 years after the incident but it says in the last article that he passed away. He must have faked his demise at the time.
In the sawmill scene during the Dead and Shoulders segment, Bart and Lisa's tongue color palettes change from red to dark brown.