Originally conceived as a direct sequel to Jumanji (1995). The visual effects supervisor on that film, Ken Ralston, was lined up to direct before Columbia abandoned the project in favor of adapting Zathura.
The beginning and end of the movie were shot on the same, intact, set. Throughout the movie the set was damaged and destroyed forcing the film to be shot in sequence except for the beginning and the end.
Josh Hutcherson, Jonah Bobo and Kirsten Stewart would all end up starring in films in which Julianne Moore would play their mother. Hutcherson in The Kids Are All Right (2010), Bobo in Crazy, Stupid Love (2011) and Stewart in Still Alice (2014).
Near the beginning of the film, Tim Robbins walks into Kristen Stewart's room. When he walks in, a "Tenacious D" poster can be seen behind him on the wall. Tim Robbins played a part in the film "Tenacious D and the Pick of Destiny" a year later.
Despite not being a sequel to Jumanji (1995) there are however some references to the film. *Both feature an event when landing on a corresponding space. *The players must finish the game in order to return to reality.
In Kristen Stewart's first scene, she mentions to her dad: "we should have never rented Thirteen." Thirteen stars Nikki Reed, a future costar in the Twilight saga. It was also directed by Twilight director, Catherine Hardwicke.
(at around 53 minutes) Walter accuses Danny of cheating after noticing his piece is ahead of Walter's; Danny constantly insists he did not cheat. The sequence of the two boys' turns leading up to this point is as follows: Danny got a total of 28 turns (5, 4, 7, 6, 6) and Walter got a total of 37 turns (9+move ahead 2 spaces, 8, 6+move ahead 4 spaces, 8). Since Walter got the more amount of turns than Danny, this places Walter's piece ahead of Danny's, which proves Danny did, in fact, cheat. If you pay close attention (at around 43 minutes) where Danny is seen taking his turn before Walter's turn in which he accuses Danny of cheating, you'll notice Danny's piece lands on a spot different than the one shown right before Walter says to Danny, "I was ahead of you.", which further proves his accusation.
When Walter is telling the Astronaut that he is eating all their food, and that he should leave, the Astronaut says, "The card said 'Rescue stranded astronaut'" This is a hint towards the Astronaut being an older version of Walter, considering the Astronaut hadn't read the card. He knows what the card said because he himself got the card many years ago.
As Danny's ship reaches the final space on the game board, and the large Z starts spinning, he's heard shouting 'Zathura!'. This is most likely a reference to Jumanji (1995) (also based on a book by 'Chris Van Allsburg') as in that game, in order to end it, the winning player must shout 'Jumanji!' when they reach the final space.
The Astronaut being Walter is hinted at in the kitchen scene when Walter yells at Danny, "Who's brother are you, his or mine?!" Foreshadowing that they are the same person and Danny's brother is both of them.
There are a couple Easter eggs that give away scenes related to the film A Christmas Story (1983), given that Peter Billingsley, who plays Ralphie in that film, is a co-producer in this film. In a beginning scene when the father tells Danny how special he is, a bobblehead that resembles Ralphie is visible on Danny's desk. In the final scene before Zathura is reached, the leg lamp is visible behind the characters.
The numbers spun by Danny and Walter (respectively) are as follows: (5, 9+Move ahead 2 spaces), (4,8), (7,6+Move ahead 4 spaces), (6,8), (6,0 [walter get's ejected]), (8 - Move back 2 spaces, 9), (9 - Move back 1 space, 3 - Move back 3 spaces), (1 + Move ahead 9 spaces - Danny wins the game).
After he leaves his to get a new piece of paper after it is spilled on by Danny, the dad is absent for most of the film and does not re-appear until the end when he gets Walter and Danny ready to go to their mother's house.