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.
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.
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.
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).
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.
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.
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).