Bendee Boo and the Mystery Crew is a parody of "Scooby Doo Meets The Harlem Globetrotters"
Fry, voiced by Billy West, is portrayed as Shaggy in Bendee Boo and the Mystery Crew. Funny enough, Billy West was the voice of Shaggy in "Scooby Doo on Zombie Island".
Purpleberry Pond is a parody of "Strawberry Shortcake" & "The Smurfs."
G.I. Zapp is a parody of "G.I. Joe".
During the GI Zapp segment, Nixon asks if there is any equipment for editing tape. This references the infamous missing 18 minutes of audio from the White House tapes.
The episode does on multiple occasions hint at some production "trademarks" during the cartoons, such as:
Leela mentions that they are going through the "Repeating Forest", referencing the 'cost-effective' practice of using the same background over and over. There are several instances during Bendee Boo.
The laugh track plays whenever Fry speaks, as it generally did on Scooby Doo whenever Shaggy spoke. (In Bendee Boo, the characters are aware of the laugh track, mentioning that it doesn't seem to correspond with anything funny happening.)
In Bendy Boo you can see dirt on the animation cel when the Delivery machine is moving.
In the establishing shot before the bed scene the camera is pulled too far and a writing can be seen on the Background ce: "Establishing Shot - Use in every Episode".
In the Purpleberry Pond segment, the characters talk about their "healthy Purpleberries" with cut-in commercials of the sugar-saturated Purpleberry Cereals. In response to the parents' initial concern, the show makes it seem like the product is nutritional, but the cereal is plainly unhealthy. Also the Cereal Girl in the commercial gets wider every time.
Also lampoons the fact that many cartoons were just used as cheaper and more influencial advertisments.
The GI Zapp segment (as the cartoons it parodies) presents ultraviolent content as children's programming, with the idea that it's ok because it isn't "real".
Nyxon says "Beam me up, Scotty", the phrase Spock says to Scotty when in need of teleportation to the Starship Enterprise in Star Trek.
The 'PSA' at the end of the episode parodies the The More You Know PSAs that were run during NBC's children's programming