Yes, Dear: In "Arm-Prins", Greg is left to look after his son, Sammy, while Kim tries to sell her titular invention, Greg has Sammy watch a VHS of Blue's Clues while he runs to the bathroom after not peeing for six hours as a result of drinking too much iced tea. Turns out Sammy really wants to watch it, as Greg is forced to sit through it over 20 times. This eventually leads to him dreaming about being stuck in Steve's house. In The Stinger, Kim discovers Steve Burns is in her bed, and they make out.....in front of Greg.
Battle for Dream Island: In the Season 1 episode "The Glistening" and the Season 2 premiere "Yeah, Who? I Wanna Know", Leafy Blue-Skidoos to Yoyleland via a Map of Goiky. She does it again in episode 26 of Season 4.
SuperMarioLogan: In "Black Yoshi's Kids!", when Mario gives Black Yoshi his welfare check, Black Yoshi sings to the tune of "We Just Got a Letter":
We just got some welfare, We just got some welfare, We just got some welfare, How much is this check?
The Fairly OddParents: One of the shows that the characters travel through in the TV movie "Channel Chasers" is a parody of this show called Clint's Hints hosted by an overly-enthusiastic guy with a shaving cut in a striped polo shirt named Jeff (played by Jason Marsden).
MAD: In the sketch "Avaturd", Jake is attacked by a giant Blue.
In a sketch on Robot Chicken, Steve looks at the clues (a set of teeth, a squirrel foaming at the mouth, and a shotgun) and comes to the conclusion that Blue got bitten by a rabid squirrel and is begging for a mercy killing. But as he goes up Blue and pulls out the gun, Steve lets it slip that he's actually doing this because Blue was planning to replace him with "some spotlight stealing son of a bitch named Joe." The sketch ends with Steve about to shoot Blue, only for her to lunge at him with a broken bottle.
The Simpsons: In "Little Girl in the Big Ten", Lisa says that her college friends "don't have a 'Blue's Clue'" that she's only eight years old.