One page from a comic of Rick and Morty has Morty looking over a tabletop game called Starhammer◊, which features a mascot that looks remarkably like a S.M. Terminator wielding a power sword.
In "Chapter 14: Vytal", after Jaune supercharges Nora with his Force lightning during JNPR's tournament match against BRNZ, Nora screams "KILL! MAIM! BURN!" while charging at Brawnz and Roy.
While resisting the influence of the Mask of Nihilus, Alix roars out "Loyalty...is its own reward!" This is a reference to Lion El'Johnson, the Primarch of the Dark Angels.
In an unpublished epologue to the final Doctor Who New Adventures novel, The Dying Days, a future incarnation of the Doctor teases Jason Kane by claiming that the last time he saw Bernice Summerfield, she was being inaugurated as God-Empress of All Human Space.
The Dresden Files: In the short story "The Warrior" we learn that Father Forthill, Michael's handler in his war against evil, is technically an inquisitor. Of the Ordo Malleus, to be more specific.
Rivers of London: In False Value, when Peter learns that his American counterparts call themselves the Ordo Machinis Spectandis, he can't resist making 40K jokes.
The murder victim in Peter T. Garratt's detective story "The Next Big Thing" was a writer who did tie-in novels for a wargame called ''Battlespear 20,000", described as involving fantasy races, but in space.
Doctor Who: The human culture depicted in "Nightmare In Silver" is an empire with an "Imperial Guard" that casually destroys whole planets to deal with alien infestation, and their Emperor is virtually worshipped. Even the uniforms bear a substantial similarity, and they wield laser weapons. As a Mythology Gag within a Shout-Out, the Emperor's full name is Emperor Ludens Nimrod Kendrick Cord Longstaff the 41st.
The Expanse: When discussing plans to rescue the Nauvoo and refit it into a warship for the Outer Planets Alliance during "Fight or Flight," Drummer sarcastically tells Fred Johnson that "A cathedral converted into a warship sounds like the heart of a great and lasting nation."