The whole show starts and middles as a Shout Out to Jonny Quest.
Hank's outfit is clearly based on that of Fred from Scooby-Doo, a fact that other characters have remarked on, and Dean's clothes and haircut are reminiscent of Peter Parker's from his debut. Dean's pajamas are... Spider-Man themed. Hank's are Aquaman, and as a somewhat beefy blond he actually looks a little like the King of the Seas. To drive it further home, the apartment Dean lives in during his summer internship at Impossible Industries is almost exactly the same as Peter's from the movies.
Star Wars is a particularly popular subject. Usually patently obvious. This escalated to the point that, upon seeing the sheer volume of them while recording commentary on every episode of Season 2, Doc Hammer and Jackson Publick dared each other to avoid direct Star Wars references for all of Season 3, with the loser having to revert to their eighth-grade haircut.
This show does lots and Shout Outs to various bands and musicians. Led Zeppelin, The Stooges, The Buggles, Duran Duran (not named but directly referenced), Bjork, Adam and the Ants, Depeche Mode, The Residents, Ladysmith Black Mambazo, and Jesus Jones have all been explicitly name checked. David Bowie was alluded to at least three times in various fashions before his appearance at the end of season two with Klaus Nomi and Iggy Pop.
In "What Goes Down Must Come Up", the first of the Rusty's that Dr Venture comes across has the same hairdo and outfit as the singer in The Prodigy's video for Firestarter, which includes running at random in underground tunnels.
At one point, Henchman #21 tries to get Henchman #24 to team up with him as "Jet Boy and Jet Girl", just to make a reference to a French indie band despite neither of them qualifying as "Jet Girl".
Dr Orpheus' observation in "Self-Assisted Suicide" that "the doors of perception have opened all at once" could be counted as a double Shout-Out: once to the book of the same title, and once to The Doors, who named themselves after said book.
The occasional ray-gun sound effect is a dead ringer for the ones in He-Man.
Jean-Claude LeTueur's supervillain costume and history as a big game hunter/comic book nerd all harken back to Spider-Man foe Kraven the Hunter; Kraven's costume has a lion head chestpiece and leopard skin pants, LeTueur's has an elephant head and zebra skin.
Russel Sturgeon is explicitly based on Quint from Jaws in voice and appearance, his costume resembles that of Aquaman, and his entire MO as a fishing themed aquatic villain is a take on Aquaman villain the Fisherman.
While showing off the Order of the Triad merchandise, Doctor Orpheus claims that the Jefferson Twilight figure is actually just a repainted Mego doll of The Falcon. Meanwhile, the Alchemist figure is stated to be a kitbashedSpock doll.
In general, the three assassins sent after Brock are all shout outs to the different kind of villains of Comic Book Ages. Go-Fish is a shout out the Golden Age, Le Tueur to the Silver Age, and Herr Trigger to the Bronze to 90's Darker and Edgier style of villains.
Le Tueur's name is a reference to a comic by the same name by French writer Matz, about an unnamed assassin.
And Molotov's list of targets are actually the writers and artists of the original Marvel Comic given to Dr. Venture by Henchman #21 earlier in the episode.
The fourth season premiere contains a lengthy shoutout to the climax of Raiders of the Lost Ark. Complete with "Don't look, no matter what happens," and Nazi face-melting.
When Colonel Hunter Gathers arrives at OSI during Operation P.R.O.M.:
Doe: That's none of your concern Mr. Gathers. Gathers: That's Colonel Gathers to you. Cardholder: Oh yeah? Well in that case, I'm President Cardholder, and this is my associate, Emperor Doe. Doe:God Emperor Doe.
Minor villain White Noise is a somewhat convoluted Shout-Out to Glowworm from Astro City. Their mutation is vaguely similar, but while Glowworm was a black man before his accident (and is angered when he was portrayed as white supremacist in an in-universe comic), White Noise is simply a white supremacist. Definitely could be chalked up to coincidence, but not likely given the sheer number of comic shoutouts in the show.
SPHINX, while more directly based on Cobra from G.I. Joe and by proxy Hydra from Marvel Comics, seems a little too similar to Astro City's own Nebulous Evil Organization, PYRAMID. The Ancient Egypt motif, as well as the color schemes and general appearance of the uniforms, speak for themselves.
Captain Sunshine is not only a shout-out to Superman and Batman, but also Birdman, particularly in the way Birdman's powers are restored following his re-exposure to the Sun in some convoluted manner.
Captain Sunshine and the rest of the Action News Team/Super Gang are based on the Freedom Fighters, a relatively obscure team of DC Comics heroes — Captain Sunshine himself is the Ray, US Steel is Uncle Sam, Brown Thrasher is the Black Condor, Ghost Robot is the Human Bomb, and Barbie Q is Firebrand.
There are several references to 1990s era Nickelodeon shows, from Hank demanding of Dean's disembodied head "Yeah, Clarissa, explain it all" to 24, mad over 21 finally getting rid of his skull, asking 21 if if he's really just going to bury it and "declare this meeting of the Midnight Society over."
When Dr. Killinger cuts Dr. Venture so he can sign a contract in blood, Doc references the 1970s KISS comic book, which allegedly had the blood of the band's members mixed in the ink.
Brick Frog (a villain trying out for The Revenge Society in Bright Lights, Dean City) is in name a reference to the indentation in a standard brick and a villain from the live-action Tick show and in appearance a reference to the relatively obscure Marvel hero Frog-Man.
Ladyhawk Johnson and Lyndon Bee, a woman who turns into a hawk at night, and a man who is a bee by day, is a reference to the movie Ladyhawke and the former president and first lady Lyndon B. Johnson and Lady Bird Johnson. "I shall not seek, or accept, your escape." Ladyhawk also has large angel wings sprouting from her back and a harness like the X-Men character Angel.
In episode 3 of season 2, Brock begins to slap a plastic surgeon that performed a sex change on Col. Gathers, telling him that "he was like a father to me!" The surgeons sobbed responses in between the slaps that "he's your mother! Your father! Your mother! Your father! Your mother and your father!" is taken almost verbatim from Chinatown.
At the start of S5,E5 Headshot refers to Molotov as "Hit-Girl". It's reinforced later in the episode when you learn that she was trained as an assassin by her father.
Fridge Brilliance when you realize she basically is Hit-Girl and Mother Russia rolled into one!
In the Season 4 episode Every Which Way But Zeus, a lot of characters get together to take down the episodes Big Bad. All of them are given codenames. Two characters in one body are given the names Kenan and Kel.
In the Season 5 episode Bot Seeks Bot, Dragoon's choice of torture reflects the nightclub scene from Requem For a Dream
"Ass to Ass!"
In "Bright Lights, Dean City", Rusty is trying to pitch a Broadway musical based on his life. While hammering out the score in Dean's apartment, he's joined by the Ventureverse's Spider-Man expy, who sings along. When Rusty asks him about his skill as a singer, not-Spidey mentions that he was once in a production of "The Sound of Music". The actor who played Spider-Man in the 1970's live action television series, Nicholas Hammond, was previously famous for playing one of the Von Trapp children in the original Sound of Music film.
When Hank and Dean run away from home on their hover bikes in the last episode of season one, great parts of this sub plot reflect Easy Rider, with one of the most obvious being Hank and Dean's helmets.