The Boondocks referenced the series in its early years.
In one strip, Huey sees Robert watching television. Huey complains that the series for black audiences are as abhorrent as The PJs, and Robert asks Huey what does he have against The PJs.
In one story arc, Huey and Caesar watch Fat Albert and the Cosby Kids after the announcement of a live-action Fat Albert movie. Towards the end of the arc, Caesar points out how the titular Cosby Kids are named after some sort of personality disorder, prompting him to ask Huey why don't they just watch The PJs.
Family Guy: Not in the series itself, but a segment from FOX's 25th Anniversary Special has the cast attending the celebration with the network's stars. When Peter points at another table and asks Cleveland why he isn't sitting with his new family over there, he clarifies that they're actually The PJs.
Futurama: "I Second That Emotion" and "The Luck of the Fryrish" feature Thurgood on the sewer manhole cover, referencing the intro to The PJs. Per David X. Cohen, the Futurama crew were fans of the show and were upset at it being Screwed by the Network. note In response, the writers of The PJs put an image of Fry on the back of a milk carton in "Cliffhangin' with Mr. Super".
Robot Chicken: "Celebutard Mountain" features a proposed "final episode" of the series, in which Thurgood gets pulled over for picking up a transvestite hooker (referencing Eddie Murphy's 1997 arrest for that).
