The Horton quote "I meant what I said, and I said what I meant: An elephant's faithful one hundred percent," is actually from "Horton Hatches the Egg," another Dr. Seuss story featuring the enduringly faithful elephant.
When Horton is turning his ears into different hats, one of the hats is one worn by Bartholomew Cubbins in the Dr. Seuss book "500 Hats of Bartholomew Cubbins".
Amy Poehlers character is named Sally O'Malley, which is also the name of a recurring character on "Saturday Night Live (1975)" played by Molly Shannon. Both Poehler and Shannon got their careers started on Saturday Night Live.
The basket that Jo-Jo McDodd jumps into to reach the slingshot which ascends him to the old observatory, is actually a part of a giant Alexander Calder sculpture known as a "mobile."
In the scene where the Mayor of Whoville consults Dr. Leroux about what would happen if Whoville was a tiny spec in space, you can see that Dr. Leroux is holding up a piece of paper. On that paper, the first paragraph is just random typing. However, the following paragraph, it reads: "Clerk Maxwellies which othe machines, ranging fromag-neticles variety. Aside tranging. Electrodynamics at rea of theorology of the for can ever..."
The Mayor receives a goldfish in a fishbowl from a Who who looks remarkably like the Cat In The Hat (he is only seen twice, briefly - once from behind, and later from a distance - and his hat has blue stripes instead of red). Later, just before the first attack by Vlad, the Mayor is resuscitating the fish. When the fish lands back in his bowl, he leans on the side of the bowl just like the goldfish in The Cat In The Hat.
When the Mayor is showing Jo-Jo the portraits of their family the last one of caveman who is painted on a set, evidenced by the lights at the top and creatures hanging from the ceiling by string.
When walking in Whoville, the mayor is saluted by a character who tips his hat, which is the hat of 'The Cat in the Hat Comes Back' with multiple little cats inside it.
Katie, the yellow fluffy animal, is supposed to be a tiny yak. The awkward greeting she makes was just one recording that was used several times throughout the movie.