Title: Pirate radio also refers to bootlegging music. It also refers to radio stations who operate illegally, that is, without any required permits. Such stations exist in countries where radio or television is state-controlled.
Ember says "Where's the splat?", which may be a reference to a similar line in Disney's Peter Pan.
Early in the episode, Sam calls Youngblood "Short John Silver", a take on Long John Silver, the pirate captain from the novel Treasure Island. Long John Silver is also the name of a popular seafood chain.
When the parents that were not lured aboard were captured, Danny told the kids, "If you want your parents back, you're going to have to follow my lead!" This is a reference to Jimmy Neutron Boy Genius when the Yolkians grab the Retroville adults.
The music that begins playing at 8:02, when the other parents are packing for the cruise trip, is a soundalike version of "Walking on Sunshine" by Katrina and the Waves.
Title: A wordplay on "rain storm", which is similar to a thunderstorm.
The "nerd poker" looked suspiciously like Yu-Gi-Oh cards.
The ghosts on the Ecto-Exodus Alarm strongly resemble the ghosts found in Pac-man.
After Danny asks the ghosts how Sam and Tucker crammed all of them into the Specter Speeder, Ember comments, "Hey, you ever been inside your stupid thermos? Compared to that, it was the Taj Mahal in there!". The Taj Mahal is located in India and is one of the Seven Wonders of the Modern World.
When the Danny clones beat up Pariah Dark, the word "Zark!" appears as an exclamation. In The Hitchhiker's Guide to the Galaxy, "zark" is used as a swear word.
The plot and final battle resembles that of the Age of Apocalypse arc from the X-Men comics, the most notable example of this is how the protagonists have to lock the antagonist in a casket to defeat him.
Title: A play on the movie title, Star Wars Episode I: The Phantom Menace. It is widely known that the shows creator Butch Hartman is a Star Wars fan. This was later clarified during the Fairly OddParents special Wishology!.
The part about Danny being the only one being able to see Youngblood shares a similar concept as that of the movie The Sixth Sense and the Twilight Zone episode Terror at 20,000 Feet.
Tucker's tape recorder looks remarkably like an iPod.
Bearbert Einstein is a play on Albert Einstein, right down to their similar appearances.
The "pole thing" (where Danny and then Skulktech 9.9 are falling to only catch a pole to break their fall) is a reference to the Spider-Man comic series. Both times, the protagonist loses his powers before catching onto the pole.
When Valerie blasts Dark Danny into the street, he sticks his hand through the dust and then clears it, this is homage to One Piece when Luffy knocks back CP9 member Blueno into the side of a building and he does the same motion.
Dark Danny is similar to the X-Men villain Onslaught, who came to existence from Professor X's dark side combined with Magneto's consciousness. He also bears some resemblance to the Spider-Man villain Venom, which is particularly stressed when he extends his tongue.
Clockwork's ending speech is from Neil Gaiman's Sandman character, Delirium.
Dark Danny also slightly resembles the superhero Freakazoid, from the 1995 cartoon of the same name. Interestingly enough, David Kaufman, the voice of Danny, did the voice of Freakazoid's secret identity, Dexter Douglas.
When seeing the actions of Dark Danny, one part shows him lifting a tank while running around. In the shot, the way Dark Danny's holding the tank and the way one of the civilians is running is an homage to Action Comics #1, the first appearance of Superman.
Title: Flirting with disaster means to take unnecessary risks. The title also could have most likely been a reference to the hit 1979 song by Molly Hatchet.
Tucker says that one of his chips makes his PDA a GBA, which stands for Game Boy Advance.
Technus, while inside the computer hub, is in a situation remarkably similar to the one in the end of the famous sci-fi cult-classic "Lawnmower Man." In the latter, the computerized protagonist is trapped in a computer hub and tries (in vain) to break a firewall and be released into the world. Like Technus, the protagonist of "Lawnmower Man" initially thought the task would be simple, but it was not.
Title: A beauty mark is a dark, facial mole that - if placed properly - is considered attractive.
In this episode, the prince's name is Aragon. This may be a reference to the Inheritance trilogy, a popular series by Christopher Paolini, where Eragon is a dragon-riding swordsman (This link is later enforced when Dora transforms into a blue, Saphira-like dragon with Sam riding astride her back).
The glass slippers Sam tries on are similar to the ones wore by Disney's Cinderella.
If you replace the first 'a' in Aragon's name with a 'd', it spells Dragon.
The restaurant where the '80s party takes place is called Material Grill, a wordplay on Madonna's hit song, "Material Girl". A further reference to the singer is when Maddie dresses as '80s Madonna for the party while Jack goes as Flavor Flav.
Danny and his parents dance the Moonwalk and the Robot during this episode, both made popular by Michael Jackson.
Title: "Double Cross My Heart" refers to the English idiom "Cross my heart (and hope to die)" which is usually used to emphasize that something is the truth. "Double-cross" means to betray someone.
"A Match Made in Space" is seen inside the bookstore Sam and Gregor visit. "A Match Made in Space" is a fictional book made by the character George McFly in the Back to the Future trilogy.
Edward Gorey is also mentioned, who unlike the above is a real life writer and artist.
When spying on Sam and Gregor eating spaghetti in the mall, Danny comments "If they share a strand of that spaghetti, I'm gonna hurl," a reference to the Bella-Notte scene in Disney's Lady and the Tramp.
Also in the mall, when the Guys in White run to find whatever set off their wristwatches (Danny), you can see the Abyss store that has a banner that reads "Fleecy Tees Sale!", a reference to episode 2 (Parental Bonding). This could also be a goof, since the saleswoman in that episode said that the line of tees had been discontinued. There is a chance that they hadn't sold out, though.
The Reality Gauntlet and Reality Gems are a complete parody of the Infinity Gauntlet and Infinity Gems from Marvel Comics, right down to the memory-erasure at the end.
Gothapalooza is a spoof of the Lollapalooza music festival.
Dumpty Humpty is a reference to the nursery rhyme Humpty Dumpty. Them coming out of an egg is a play on the character Humpty Dumpty, who is most often portrayed as an egg.
There are also several homages to Batman, most notably the resemblance between Freakshow and the Joker. This is also evident when Freakshow exclaims: "Look what the bat dragged in" - A quote frequently uttered by the Joker.
Lydia's name and powers are a gag taken from the song Lydia the Tattooed Lady.
The comics convention that Team Phantom goes to is called the "San Diego Comics Fab", based off of the San Diego Comic Con.
When Danny says to the Guys in White at the end "He's not the ghost you're looking for" (in reference to himself) it parodies Star Wars Episode IV: A New Hope, when Obi Wan uses the Jedi Mind Trick on a pair of stormtroopers.
Danny's comment on the lifeless Robot Train cars, "What're they gonna do? Rust on me?" is a reference to a line said by King Arthur to the Black Knight after cutting all his limbs off in Monty Python and the Holy Grail; "What're you going to do? Bleed on me?"
The space shuttle scene was probably reference to the then upcoming STS-121 mission, flown by Shuttle Discovery.
When Freakshow brings the Robot Train cars to life, he says, "And Freakshow said, 'Let there be life!", it is a reference to the book of Genesis, the first book of the Bible.
When Empress She-Wolf says "You shall not pass!", it is most likely a reference to the same quote said by Gandalf from The Lord of the Rings.