Y: The Last Man. In a flashback to when 355 was first recruited, the previous Agent 355 introduces herself as such, adding: "I know, it sounds like something out of Get Smart." In a Brick Joke, her recruit later takes the codename Agent 86 before becoming the next 355.
Teacher's Pet: When Pretty Boy and Mr. Jolly try to go to Florida to rescue Spot, they go a little too far and end up in Cuba instead, leading Pretty Boy to quip, "Missed it by that much".
Dancing Trees: Nicky suggests that Martha wear makeup, to which she says, "Code Name 99 wore lipstick. She used to talk to it." Nicky later tells Detective Velez that Martha and her mom used to watch Get Smart together.
That '70s Show: In one episode, Eric openly states he's turning on Get Smart over a more highbrow program
Buffy the Vampire Slayer. In an episode involving Native American ghost warriors, Spike says to their leader: "Sorry about that, Chief!"
Whose Line Is It Anyway?: One episode of the original US run had Drew Carey's Couch Gag be introducing the contestants with catchphrases from Get Smart before their names (though one of them was "It will never, ever happen again", which wasn't used nearly enough to really be considered a catchphrase).
In "Last Exit to Springfield", the scene of Mr. Burns going to a high-security room to cut the town's power parodies the title sequence.
In "I'm Goin' to Praiseland", Comic Book Guy gets a vision of his personal heaven in which he is Mr. Spock, and Lt. Uhura tells him that she, Catwoman and Agent 99 all want to make out with him.
The Couch Gag for "Bart vs. Lisa vs. the Third Grade", "The Fat and the Furriest" and "A Star is Torn" is a parody of the Get Smart opening, in which Homer enter the phone booth and drops onto the couch.
