SpongeBob SquarePants
From Tardis Wiki, the free Doctor Who reference
The Tenth Doctor mentioned SpongeBob SquarePants when Rose Tyler asked him if all stories were based on disappearing time traces. (PROSE: The Stone Rose)
Rory Williams referred to Francesco as a "big, stupid, great Spongebob." (TV: The Vampires of Venice)
Behind the scenes
David Arnold composed music for the SpongeBob SquarePants series from 1999 to 2001.
Christopher Ryan and Nigel Planer both made guest appearances in the episode "Chimps Ahoy".
Robin Sachs made a guest appearance in the episode "Mrs. Puff, You're Fired".
David Hasselhoff appeared as himself in The SpongeBob SquarePants Movie.