Angel: In the second season episode "Belonging", The Host explains he also goes by the name "Lorne":
Lorne: Though I generally don't go by that because - green. (he points to his face) Cordelia: Huh? Angel: (smiles) Right. Lorne Greene. (Cordelia and Wesley stare at him blankly) Bonanza? Fifteen years on the air not mean anything to anyone here? Okay, now I feel old.
The Goodies and the Beanstalk opens with the burning map of Bonanza before Graham stamps out the fire and puts a map of Cricklewood over the charred remains. "...but in Cricklewood in 1973, the Goodies have fallen on hard times."
Futurama: In "Where the Buggalo Roam", Bender sings a ditty to the tune of the Bonanza theme while the crew goes to catch rustlers on Mars.
Garfield and Friends: In "The Lasagna Zone", one of the TV shows Garfield travels through is Bonanas, with a picture of a man riding a banana-like horse.
The Simpsons: The Couch Gag for "We're on the Road to D'oh-where" and "Rome-Old and Julie-Eh" parodies the Bonanza opening.