Marble Madness is one of the games referenced in Tenacious D in The Pick of Destiny when Jables makes his way through a maze of deadly lasers.
Web Original
In Kickassia, Lord Kat - in his role as the eponymous nation's overseer of trade - believes that China would be willing to trade a third of their military for one copy of Marble Madness.
In The Nostalgia Critic's review of James and the Giant Peach, during the scene where the Centipede causes the titular peach to roll down the path to Aunt Spiker and Aunt Sponge's house, the Critic says, "Oh, hey, great! The movie suddenly turned into Marble Madness!", and plays background music from the game.
The title of the Steven Universe episode "Marble Madness", about the Crystal Gems fighting spherical robots from space, is likely a reference to this game.