One of the visuals from the final sequence seems to be taken from the 1985 film The Quiet Earth.
Dandy becoming a Buddha in space 5.67 billion years into the future refers to the ending of a 1976 manga◊, Ankoku Shinwa (also known as Dark Myth).
Episode 8: The Lonely Pooch Planet, Baby!
Meow goes searching through the EXACT SAME FRIDGE from the Cowboy Bebop episode "Toys in the Attic", which was launched into space at the end of the episode. He even gets attacked by a blue mold inside, then eats it just like Ed did at the end of that episode.
Episode 10: There's Always Tomorrow, Baby!
At the beginning of the episode, Meow has what appears to be a McDonalds cup.
Other foodstuffs present are Loy's (Lay's chips), Pocky and a can that resembles Pringles.
The appearance of the Armed Legendary Equipment Legendary Giant Weapon is based on the Ideon in the Space Runaway Ideon series. This is perhaps no surprise given that veteran mecha designer Kunio Okawara was involved in the episode's production.
It also opens up the panels on its chest to reveal a lion's head that looks remarkably like that of either Daltanious or GaoGaiGar.
The A.L.E. also has a head and barrels reminiscent of a Guncannon.
Dandy's response of "there is a fourth" when the crew discover someone has come aboard the ship references the Japanese title of They Were Eleven.
QT's "Final Dandy" quiz show is a parody of Quiz Millionaire (the Japanese Who Wants to Be a Millionaire?). QT uses both the "is that your final Dandy?" catchphrase and host Mino Monta's famous habit of staring silently at contestants in suspense before announcing the right answer.
Dandy, QT, and Meow end up jumping from one universe to another, jumping through various animation styles, character designs, and laws of physics as they go. One of the universes was Attack On Dandy. In another, they're Mobile Suit pilots, with Dandy specifically being a Char Clone... literally.
Ukeleleman and his photorealistically-textured mansion would not feel out of place in Courage the Cowardly Dog: His character design, his unsettling movements, his behavior stemming from an intense and tragic psychological need, his ethnic-sounding leitmotif, his nonviolent yet creepy powers, his highly delusional behavior, the perpetual calmness of his voice, the attacking of the two characters closest to the protagonist forcing the protagonist to carry them out and flee, a surreal One-Winged Angel mode, and his spiritual fulfillment upon his defeat all parallel Courage.
During the space-surfing scene, the Space Battleship Yamato can be seen rising and crushing Dr Gel and Bea as it falls back into the River of Time.
Episode 17: The Transfer Student is Dandy, Baby
The music in school premise of the episode is pretty much GleeIN SPACE!.
It's given a Shout-Out in the dub after QT explains to Meow what the school is really like: "Oh, the glee he must be feeling".
Several scenes within this (especially the 'running up a steep staircase wearing geta' bit) are a callback to GunBuster in particular, and comes complete with a gloriously cheesy vocal theme that parodies the kind used in any number of similar montages in 70s and 80s anime.
Episode 19: "The Gallant Gentleman In Space, Baby!"
Dandy and Meow try to convince a bodyguard that they are both female, and quickly add "Everyone has a fault or two!", referencing Some Like It Hot's closing line ("Well, nobody's perfect!").
Episode 20: "Rock 'n' Roll Dandy, Baby!"
The names that Dandy and Johnny propose for their nascent band are all shout-outs to different Japanese musicians and album covers, most notably Tetsuya Rave Factory (TRF for short).
Johnny may as well be Johnny Yong Bosch incarnated within the show itself. He even has several features shared by some of his most famous roles.
He has red hair like Sasori and Ichigo Kurosaki. He also kicks people a lot like Ichigo, and his wardrobe wouldn't be out of place in Ichigo's closet.
He's the commander of the Jaicro Empire and pilots a mech like Lelouch Lamperouge. During one scene, a waiter even mentions that the dish he's brought comes straight from Britannia, and his commander outfit is almost exactly identical to the one Lelouch wears after becoming Emperor in R2.
The entire episode's premise is about him forming his own rock band. JYB actually does have his own rock band (Eyeshine).
While trying to get inspiration for a new song, there are sudden flashes that show a close-up of his eyes, referencing Lelouch as well as Yu Narukamiand Tohru Adachi.
Johnny setting his guitar alight with flame breath is of course a shoutout to KISS's Gene Simmons.
Dandy's hair catching fire during the concert brings to mind a similar accident to happened to Michael Jackson during the filming of a Pepsi commercial.
Episode 22: We're All Fools, So Let's All Dance, Baby!
The planet the dance festival takes place on is Planet Grease.
When Dandy is bribed into posing as the Dancinian, the chief of Grease bribes him with the 2012 Agnes Lum Photo Book. Lum was a Hawaiian gravure idol whose popularity peaked during the '70s-'80s in Japan. The same photo book can be seen here◊.
Additionally, the black and white graphics used during the universe's remaking are the same as graphics used in the finale of the film AKIRA.
Episode 23:"Lovers Are Trendy, Baby!"
In the beginning of the episode at the Alien Registration Center, Dandy and crew try to register an alien which according to Scarlett is commonly found at Nebula M78. The alien is so big we don't see all of it except for its silver boot.
The train preventing Scarlet and Dandy from seeing each other again parallels one of the final scenes in the film 5 Centimeters per Second, where Tōno and Shinohara miss seeing each other while the cherry blossoms fall. Both scenes will make viewers resent trains forever.
Episode 24: "An Other-Dimensional Tale, Baby!"
Dr. Gel and Bea get sucked into the 2D universe. When he engages enemy ships inside the universe, the battle plays out like Galaga.
The premise of this episode is basically Flatland.
Planet Abbot is named after Edwin Abbott, the author of Flatland.
Episode 25: Dandy's Day in Court, Baby!
During the cross-examination of Meow, it's revealed that Dandy once tried to sell Meow at a pet shop, couldn't get a lot of money, and decided to keep him on the crew. This is much like how Ein joined the crew in the second episode of Cowboy Bebop.
The prosecutor claims that Dandy was trying to buy a robot like R2-D2 to replace QT.
As it turns out, the almost murder was done by trying to kill the pitcher by having the bat break and the wooden shards pierce him.. Looking back at Shinichiro's previous work, it draws inspiration from Mugen's baseball game.