In the episode "Toast of the Town", The Mayor was in Professor Utonium's lab and he went up to a button and said "Oooh! What does this button do?" This was a reference to Dee Dee.
In the episode "Prime Mates", Mojo Jojo was sleeping with a Monkey doll.
The Grim Adventures of Billy and Mandy
In the episode "The Grim Adventures of the Kids Next Door", When the Delightful Reaper was getting destroyed, kids from other Cartoon Network shows were flying out of it. Dexter, Dee Dee, and Mandark were three of them. Also, in the ending credits, one of the crossover parodies was a crossover between Dexter's Laboratory and My Gym Partner's a Monkey. It was called "My Gym Partner's a Mandark" and it had Mandark swinging on Jake's tail.
In the episode "Once Upon a Toon", one of the original Cartoon Network characters was Dexter. Also, Dee Dee was seen as the one who got rid of all the old Cartoon Network shows.
My Little Pony: Friendship Is Magic
In the episode "A Friend in Deed", Pinkie's line "Ooh, what does this bauble do?" was a reference to Dee Dee.