Although Joe's shirt is a small reference to Nobuyuki Matsushima; creator Hideki Kamiya revealed via Twitter that in-universe, the letters HMD on Joe's shirt stand for "His Master's Dance" in respect to Captain Blue.
In an interview, Hideki Kamiya discussed the origins of how Dante from the Devil May Cry series became a playable character in the PlayStation 2 version of the game:
"As for Dante, we had a talk about adding him, and two days later someone went and made a model of him on their own. It was someone from the Okami team, who wasn’t even related to this project. (laughs) After that we to create his big gun, and of course it wouldn’t be Dante without his sword. Creating the very specific animations for him was really difficult. But thanks to those efforts, players can now experience the game in a whole new way."
The game's final level, "Joe & Silvia", appears to be a reference to the Star Wars film series. The enemy "Die Fighters", an obvious reference to the TIE Fighters from Star Wars, make their one and only appearance in this stage. The level takes place on a moon sized space station, not unlike the Death Star, and the level ends with Captain Blue Spoiler:revealing to Silvia that he is her father, with her denying and saying her father is dead, with Blue then telling her that deep down she knows it to be true. This mirrors the scene in the Empire Strikes Back, in which Darth Vader reveals he is Luke's father, and the same conclusion occurring.
In the level "Joe & Silvia", R.O.B. the Robot can be seen in the background. Oddly, R.O.B. was not removed in the PlayStation 2 port.
In the GameCube version, taking out a bomb but not kicking it away will result in Joe whistling the beginning of the Super Mario Bros. theme. Jumping and performing the same action results in Joe whistling another part of the song. For copyright reasons, this does not happen in any other version of the game.
During the game's credits, fake movie posters can be seen for the game's levels. Almost all of them are parodies of famous movie posters, with the exception being Midnight Thunderboy, which is a parody of the Japanese Devil May Cry box art. These include King Kong, Jaws 2, Star Wars: Episode 4, and Hunt for Red October.
The normal "henshin" hand sign in the series is simply all the fingers slightly bent. Joe's is slightly modified to have the thumb, middle finger, and pinky fingers sticking out. This hand sign spells out his initials, "VJ".
Joe's t-shirt reads "HMD". This is a reference to Nobuyuki Matsushima, the programmer of the first two Mega Man games, who often used the alias "H.M.D."
When you first meet Hulk Davidson, he will point out Joe's V-Watch and ask him, "You think you some kinda Mega man or somethin'." This is a reference to the mascot of Capcom.
The game once had the working title of "Red Hot Man," until it was changed due to copyright conflicts with the rock band, Red Hot Chili Peppers.
The PS2 remake of the game in Japan is titled "Viewtiful Joe: A New Hope". This is an obvious reference to Star Wars Episode IV: A New Hope.
Blade Master Alastor is really the personification of the Alastor sword from Devil May Cry. Many of his moves are taken from the game, and the sword and lightning he uses look very similar. When fighting Dante in the PS2 version, Alastor will berate Dante about mistreating and forgetting him.