Isabella's clothing is a very interesting Shout Out. Her clothing is reminiscent of another animated love interest, Hey Arnold!'s Helga G. Pataki. In addition, both characters keep their emotions hidden from the main character.
The boys' race car from "The Fast and the Phineas" is numbered with 42.
Just as the Doofenshmirtz blimp crashes into the broadcasting tower at the racetrack, the announcer gets cut off as he starts saying (presumably) "Oh, the humanity!", Ó la the Hindenburg disaster.
Lights, Candace, Action!Raging Bully
It's possible that the A plot's resolution was a shout out to Lilo & Stitch. To recap, Doof is holding an ice cream cone, Perry uses a whale whistle to summon a whale, which somehow leaps up into the air, over the two. The most notable thing that the whale hits is the top of the ice cream cone that Doofenshmirtz was holding, which falls through the air and, eventually, lands on Phineas's head. There's a recurring character in Lilo & Stitch who always loses his ice cream in a similar manner— once even having it knocked down by the tip of a spaceship's wing, which is the most like this scenario.
In fact, the title of the episode is a reference to the movie Raging Bull, which is about a boxer. The fact that the climactic battle is a thumb war that takes place in mini boxing ring is a testament to this.
Doof is trying to adopt a dog and Perry disguises himself as a dog to foil his plans. The pet shop owner tells him "I'm not even sure that's [Perry] a dog." It's entirely possible that this is a Shout Out to Lilo & Stitch, where the woman in charge of the kennel Lilo is trying to adopt a dog from says pretty much the same thing about Stitch.
Baljeet: Phineas and Ferb, days ago you helped me build a portal to Mars. Now I must ask for your help again. ... Help me, Phineas and Ferb. You're my only hope.
Doofenshmirtz and Perry's fight is very reminiscent of the battle between Yoda and Dooku in Star WarsEpisode 2. Doofenshmirtz even pantomimes an attempt to Force Pull a nearby wall fixture.
Day of the Living GelatinElementary My Dear StacyDon't Even Blink
The title "Don't Even Blink" could possibly be shout-outs to the Doctor Who episode "Blink". Of course, minus the creepy parts.
The heart-shaped moon in "Evil Love" could be a Kingdom Hearts shout out...or even an explanation. (Phineas and Ferb in ''Kingdom Hearts? Yes please!)
Perry Lays an Egg
The episode is full of references to Finding Nemo, specifically baby sea turtles, krill, and speaking whale language.
Gaming the System
When Doofenshmirtz traps Perry in the ball gown, the first few notes of the theme of Beauty and the Beast (notes of the line "Tale as old as time") plays.
The digitizing ray is an obvious reference to TRON, but it's probably just a coincidence that their last name is "Flynn". The game that Buford has is also similar to a Nintendo DSi. Additionally, one of the sounds in Jump & Duck is the sound that plays in Super Mario Bros. when the player gets a coin.
The Chronicles of Meap
There is a rather subtle Doctor Who gag in Out to Launch, involving Ferb's ability to "maximize inside space."
Doofenshmirtz's childhood friend Balloony also being called Colin, which was the name of the dog of a girl that Ford Prefect was implied to have liked and Ford later gave this name to a rather balloon-like security robot.
And here I thought Balloony (and his hairless 'head') may have been a shout out to another bald Colin...
Isabella tells Phineas, "I'm endangering the mission. I shouldn't have come", a quote from Luke Skywalker when the ship Han, Leia, Luke and the droids traveled to Endor.
The song in this episode is a pastiche of The B-52s.
The crowd recoiling in horror as the giant starnosed mole advances toward them is probably a shout out to Godzilla. The man who cries "Oh no, it's a hideous giant mole!" is the most obvious indication.
Oh, There You Are, Perry
Doofenshmirtz exclaims "We did it! We did it! Lo hicimos! We did it!" This bit is very similar to the "We Did It" song from Dora the Explorer (minus one "We did it").
When Irving's camera is stolen by an eel, Phineas suggests that he can take pictures in his mind and store them in his memory. Irving does this (or tries) by saying "Click!", like Cam Jansen of the titular children's detective book series.
Just Passing ThroughCandace's Big Day
When Ginger whip-cracking in the song "Wedding Adventures", she's wearing Indiana Jones's clothes.
There is another one in "Wedding Adventures" right before the whip-cracking scene. Milly is doing the idol scene from Raiders of the Lost Ark.
I Was a Middle Aged RobotSuddenly SuzyUndercover Carl
The episode begins with Phineas saying "Ha ha, gravity." This is the exact same line that Aang from Avatar The Last Airbender makes in one episode. Just a few seconds later he says they're busy 'defying gravity', possibly a reference to the Wicked song.
Also, Baljeet claims that the name of his board game is called "Spinning Tops Of Doom". Sound familiar?
The Lizard Whisperer
During Ferb's speech alludes to the famous "We Shall Fight on the Beaches" speech. It's not just Winston Churchill, though — it starts like Aragorn's speech at the black gates and ends with "we band of brothers."
A motivational speaker asks a girl if she knows what it takes to be president. She says "Yes. Yes. I. Can."
The Doof Side of the MoonSplit Personality
Candace is cloned and runs around trying to find her clone. At one point when told that her clone has gone off with her mother, she does, of all things, an imitation of Donald Sutherland's famous howl from Invasion of the Body Snatchers.
Another from this episode is the outfit Linda is trying on in the dressing room is clearly the outfit Jesus wore in the GodSpell movie.
The video game Phineas, Ferb, Baljeet, Buford, and Isabella are playing greatly resembles M.U.G.E.N.
"Permanecer sentados por favor" (Spanish for "Please remain in your seats") from the "Rollercoaster" song is a shout-out to the safety speil at the end of the Matterhorn Bobsleds in Disneyland.
At the end of the episode, they mention the phrase "Carpe Diem", which means "Seize the Day". Then they go into the last song, "Carpe Diem", choreographed by Kenny Ortega, who was the director and choreographer for the musical film Newsies, which had a song called "Seize the Day". What's more is that the set for "Carpe Diem" is reminiscent of High School Musical, another Kenny Ortega musical film.
When Phineas and Ferb are showing off their biosphere to the Fireside girls, Phineas asks, "Can we cook, or can't we?", a Shout Out to Star Trek II: The Wrath of Khan, were Dr. Carol Marcus asks "Can I cook or can't I?" when showing Kirk the Genesis Cave.
Candace's reaction to the train making it to the top of the mountain is to paraphrase The Little Engine That Could. ("I knew we could, I knew we could, I knew we could!")
Meanwhile, the episode's title references The Monkees song "Last Train to Clarksville".
Phineas' Birthday Clip-O-Rama!The Belly of the Beast
The episode eventually morphs into a Moby-Dick reference, guess which character channels Ahab and which two titular characters become the white whale. Also, the boat chasing the shark is named "Pea-quad" (the Pequod).
This episode also features a few references to Jaws, the most obvious one being when Phineas says, "we're going to need a bigger shark!" (Candace also uses the same line).
Moon FarmAsk a Foolish QuestionMisperceived Monotreme
Major Monogram has security footage of Dr. Doofenshmirtz singing a song about Shangri-La, which may be a reference to Xanadu (which featured a song of the same name sung by Olivia Newton-John and Electric Light Orchestra—the latter of whom, likely coincedentally, has a song called "Shangri-La").
Candace DisconnectedMagic Carpet Ride
The song "Aerial Area Rug" is an obvious affectionate parody of the song "A Whole New World" from Aladdin
Jeremy's mother is reading the manual for the tranquilizer dart, which includes the sentence "there are many like it,but this one is yours." Her reading the manual in the first place may be a reference to Edmund reading the manual for a cannon in the final episode of Blackadder the Third.
Doofenshmirtz can be seen playing an piano organ, he then plays a couple of familiar notes and you could have sworn he could have said What is a Platypus?!Start at 3:38
Meatloaf SurprisePhineas and Ferb InterruptedA Real BoyMommy Can You Hear Me?
There's also a brief nod to Wax On, Wax Off (which Buford, of course, fails to grasp), and the giant terracotta warrior's opening move against Doofus Khan is the Crane Stance, also from The Karate Kid.
There is a swamp in The Neverending Story. In order to cross it, you must not think unhappy thoughts. "This swamp was made for me, Ferb!"
Among the ten thousand monsters gathered by Phineas and Ferb is a Gargoyle resembling a green Goliath.
Strangely enough, the "Epic Monster Battle" song sounds a lot like Christian musician Carmen's "The Champion".
Phineas and Ferb and the Temple of JuatchadoonMonster from the Id
The title is a nod to Forbidden Planet. The opening of the episode has the kids sharing their minds; besides the obvious Star Trek mindmeld shoutout, the set-up also calls to mind Inception's dreamsharing. Near the end of that adventure, while inside Candace's mind, all the kids have to give Baljeet a 'kick', by shocking him with grammatically incorrect contractions. It also appears that Buford remained behind with Candace's primal self, in her mind's limbo. The music during this segment also bears strong similarities to Hans Zimmer's score for Inception, particularly the use of electric guitar.
The entire episode is basically a Phineas-and-Ferbified version of the movie Memento, not so much in terms of the plot, but in the way the story is told: it starts at almost the end, and works its way scene-by-scene back to how it all began, slowly revealing more of the plot as it goes. This might just be seen as an unintentional coincidence, except that at the end, Perry who is revealed to have had his memory stolen by Doofenshmirtz, finally remembers his mission because he had written a message to himself on his body before his memory was erased.
The B-plot involves a mad scientist using an experiment designed to cause chaos by exposing people's little white lies, which sounds suspiciously like the "Fibber" episode of Lilo & Stitch: The Series, another Disney cartoon.
Bully Bromance BreakupQuietest Day EverThe Doonkelberry ImperativeMeapless in Seattle
For another absolutely epic Star Wars reference, we are given the opening credits.
Doofenschmirtz's musical number has him in a white tux accompanied by a jazz band dancing in a way remarkably similar to Cab Calloway. Heck, the song might even be considered a reference to 'The Old Man of The Mountain", famously used in a Betty Boop cartoon of the same name.
May or may not be intentional, but the situation Perry and Doofenshmirtz get into (being handcuffed to each other and chased by a hunter) is extremely similar to the plot of one Danny Phantom episode. The hunter even mentions hanging them in his trophy room!
The episodes includes several references to The Shawshank Redemption, including the drainpipe escape and the prison including an inmate named Red who knows how to get things.
The basic plot is that the heroes are given the chance to vacation on an alien planet by swapping minds with its inhabitants, only to discover once the swap has taken place that they've been conned. This is very similar to the opening chapters of Robert Sheckley's 1966 novel Mindswap. In fact the phrase "mind swap" actually occurs in the episode.
DruselsteinoweenTerrifying Tri-State Trilogy of TerrorFace Your FearCheers for Fears
Monogram mentions that he and his friends have an event called "Horrific Movie Night", where watch and mock bad movies. Funny thing is that one of thr storyboard artists for the episode, John Mathot, has a similar thing called "Horrible Movie Night".
Major Monogram shouts "Great googly moogly!" Does that make him a Frank Zappa fan? (Who in turn took it from a doo-wop single, "Stranded In The Jungle" by The Vibrations.)
Phineas and Ferb Christmas Vacation!
During the opening for "Phineas and Ferb's Christmas Vacation", you can see the kids getting a yeti to decorate a Christmas tree, a likely reference to the ending of the classic Christmas special Rudolph the Red-Nosed Reindeer.
Near the beginning, when Phineas is defending the existence of Santa, his evidence references in turn the Patterson Bigfoot footage, the Loch Ness "surgeon's photo", and the Shroud of Turin.
During the montage of everyone decorating the town, Ferb is seen imitating a certain web-slinger while stringing up lights.
During the credits, a blink-and-you'll-miss-it scene shows everyone recreating the dancing scene from the A Charlie Brown Christmas.
From Summer Belongs To You
Near the beginning, the music while Phineas, Ferb, and the gang are looking at the giant map is an exact quote of a song from Chicken Run.
When Candace is expelled from S.H.E.D., Buford says you shouldn't get Phineas angry, "you wouldn't like him when he's angry," as she slowly walks away to a soundalike of the music from TheIncredibleHulk.
As the heroes get their powers back and prepare for battle, the camera does the 360-degree turnaround shot from TheAvengers, with Spider-Man and Perry the Platypus standing in for Hawkyeye and Captain America.
Hulkjeet saves Iron Man from a fall to his death in a moment reminiscent of that same film, after which Iron Man paraphrases one of his famous lines from the movie as, "We've got a Baljeet."
Stan Lee, granddaddy of the Marvel Universe and a frequent The Cameo in movies starring Marvel characters, voices an Ink-Suit Actor version of himself as a hot dog vendor.
The final shot, as the gang walks away from a trash can where Perry has discarded his superhero disguise, is a copy of a famous image from Amazing Spider-Man #50, in which the wallcrawler did the same thing.