In the episode Spa Spaz, one of the people visiting the spa is a caricature of Kirk Tingblad, the director of several Johnny Bravo episodes (including this one). He can be seen in a couple of scenes.
Among the people seen standing in line to see the world's largest cubic zirconium at the end of the episode The Johnny Bravo Affair, you can see both young Sheila (the girl Johnny fell in love with in a previous episode, The Unsinkable Johnny Bravo), as well as an elderly Sheila (as she looked in the segments set in the future in the episode The Unsinkable Johnny Bravo).
Johnny: Everything will be ok...Johnny is a good boy. I'll watch TV.
Carl: Johnny, that's not a TV it's a microwave!
Johnny: Quiet! I'm trying to watch my favorite show!
Johnny: My mom warned me there are women like you! I was hoping she was right.
Johnny (seeing he was locked inside the museum): What happened here? Guess it's only closing time. Or maybe the Sun exploded and I'm the last man on Earth! Or maybe it's only closing time.
During a scene in Biosphere Johnny, when Johnny is looking at the microwave thinking it's a TV, he mentions he's watching his favorite show "Macaroni and cheese spinning around, and around, and around, and around, and around and Eddy". The title of Johnny's favorite show may be an allusion to another one of Cartoon Network's original series, Ed, Edd 'n' Eddy.
The paintings Johnny and his Mama see in the art museum at the beginning of the episode The Johnny Bravo Affair, are parodies of real famous paintings: - "Rover Lisa" is a parody of the famous painting Mona Lisa, painted by Leonardo da Vinci in c. 1503-1506, which can be seen in Musée du Louvre, Paris. - "Sad Puppy Gothic" is a parody of the painting American Gothic, painted by Grant Wood in 1930, which can be seen the Art Institute of Chicago.
The episode The Johnny Bravo Affair is a parody of the 1968 movie The Thomas Crown Affair, directed by Norman Jewison and starring Steve McQueen and Faye Dunaway.
The episode Biosphere Johnny is a parody of the 1996 movie Bio-Dome, directed by Jason Bloom and starring Pauly Shore and Stephen Baldwin.