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!"
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.
So subtle you'll probably miss them. The Chronicles of Meap and Out to Launch have the most obvious ones, but there is a rather subtle Doctor Who gag in Out to Launch, involving Ferb's ability to "maximize inside space."
The titles "Are You My Mummy?" and "Don't Even Blink" could possibly be shout-outs to the Doctor Who episodes "The Empty Child"/"The Doctor Dances" and "Blink" respectively. Of course, minus the creepy parts.
The episode "Lotsa Latkes" has Bully Buford with a sock puppet, saying, "Hey! Who turned out the lights?" in exactly the same inflection as Proper Dave in "Forest of the Dead".
Phineas: ...and boredom is something up with which I will not put.
A second Shout Out is made during Ferb's speech in the "Lizard Whisperer" 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."
Doofenshmirtz and Perry's fight in "Backyard Aquarium" is very reminiscent of the battle between Yoda and Dooku in Star Wars: Episode 2. Doofenshmirtz even pantomimes an attempt to Force Pull a nearby wall fixture.
Baljeet's holographic message to Phineas in "Attack Of The 50 Foot Candace" references Leia's message to Obi-Wan Kenobi:
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.
"The Lake Nose Monster" features a boat named Nosebud and even has somebody drop a snowglobe towards the end of the episode.
Several to The Hitchhiker's Guide to the Galaxy, most notably their race car from "The Fast and the Phineas" being numbered with 42. There are others, such as 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...
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.
In the "Musical Cliptastic Countdown", 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.)
"That Sinking Feeling" is one to both Titanic and The Love Boat. Also, we see Major Monogram and Carl playing a game not unlike Rock Band while waiting for Perry.
In the extended version of the song "I'm Lindana and I Wanna Have Fun", (sung by the boy's mom when she was a pop star in The Eighties), she mentions that "I'm not Roxanne, I'm not Eileen, I'm not Sharona..."
In "Atlantis", 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.
In Toy To The World during one of the board meetings, there's a blink (or... stop-listening) and you'll miss it reference to The Fast Show when one of the execs says "suit you, sir!"
The name is also a shout out to a famous christmas carol.
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!)
In that same vein of thought, one of Isabella's lines in "Summer Belongs to You": "No... you're not gonna sit here and watch this beautiful sunset!" Given a certain other role of Alyson Stoner's and said role's hobby, could we have Actor Allusion going on here?
The episodes "Hawaiian Vacation" and "Hawaiian Vacation Part 2" featured many shout outs to Lilo & Stitch, including a cameo by the Fat Tourist and Candace wearing Lilo's signature outfit.
In "Hawaiian Vacation Part 2", Doofenshmirtz points out the crabs on the beach worshipping the Evolutionator, saying it was "Looking Kubricky".
The Legend of Zelda's "Triforce" logo can be spotted in Doof's lair (most prominently in "Run Away Runway" and was a button in the maze in "We Call it Maze", which in itself was very Zelda-reminiscent.
Also in "Phineas And Ferb-Busters", Baljeet claims that the name of his board game is called "Spinning Tops Of Doom". Sound familiar?
In "Split 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 God Spell movie.
Kim Possible makes a cameo appearance in the "Spot the Diff" special.
And so does Dr. Drakken in "Bullseye" at the evil-villain competition.
In "Brain Drain", the video game Phineas, Ferb, Baljeet, Buford, and Isabella are playing greatly resembles M.U.G.E.N.
In both "Nerds of a Feather" and "She's the Mayor" one can see campaign posters with Candace's face on them, posters which have a very familiar stylized look.
"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.
Two different Indiana Jones references: Ferb making the famous idol switch from Raiders of the Lost Ark in We Call It Maze, and Ginger whip-cracking while in Indiana's garb in the song "Wedding Adventures".
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.
Road Trip adds another one, when Perry and Doofensmirtz are fighting in the cab of Doofenzsmirtz's truck, the fight choreography is directly taken from Indy's fight with the driver of the German truck in Raiders of the Lost Ark.
In the second half of the 2-part episode "where's Perry" Doofensmirtz asks if the plane him and Major Monogram are on board has a life-boat on board, a stealth reference to Temple Of Doom.
The Belly of the Beast eventually turns 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).
The song itself is a style parody of the music from Run Lola Run.
In "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.
In "The Fast and the Phineas": 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.
When Perry and Doof first get hit, the song is from the climax of Leroy & Stitch.
The music guys do this a lot: during "Out to Launch", the music that plays during the trip through the asteroid field bears a striking resemblance to a song from the Star Wars soundtrack called "The Asteroid Field". It's quoted again during "Meapless in Seattle".
Near the beginning of "Summer Belongs To You", the music while Phineas, Ferb, and the gang are looking at the giant map is an exact quote of a song from Chicken Run.
In "Lawn Gnome Beach Party of Terror", there's another quote from "Under the Sea".
And yet again in "Hide and Seek", when the music during the sewing supplies sword fight is nearly lifted from Pirates of the Caribbean.
In "The Secret of Success", a motivational speaker asks a girl if she knows what it takes to be president. She says "Yes. Yes. I. Can."
In "Summer Belongs To You", when the group accidentally ends up stranded in a deserted island with almost nothing to create, Phineas goes crazy when he tries to find something to do and beat Bufford's dare. He then digs up a deep hole where he holds up a yellow sponge and a pink fish star.
In "Ladies and Gentlemen: Meet Max Modem!", the aliens that Heinz projects dance and behave like a certain group of invaders, possibly from space.
This is further reinforced by the fact that Doof says "You are being invaded, from space! By invaders! From space!"
In "Carl Undercover", 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.
David Mitchell was the voice of Mitch in "The Chronicles of Meap"
The song "Aerial Area Rug" from the episode "Magic Carpent Ride" is an obvious affectionate parody of the song "A Whole New World" from Aladdin
In "The Great Indoors" Isabella recites a Fireside Girls version of Allen Ginsberg's "Howl".
It's possible that the A plot's resolution in "Raging Bully" 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.
It's possible that "the Ferbalistic Groovatron 9000" from "Nerdy Dancin'" is a Shout Out to the Future trilogy of Ratchet & Clank, which features a recurring device/weapon called the Groovitron. Coincidentally, the "Otherdimensionator" comes close to sharing a name with Tools of Destruction's Dimensionator.
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.
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.
Unsure if this one is intentional or not, but in 'Nerds of a Feather', Buford's reaction to a holographic Phineas showing up is 'What trickery is this!?". Samurai Jack said the exact same line before he was flung into the future.
Baljeet's costume from "That's the Spirit" looks an awful lot like the creature that Daffy Duck is turned into in one of the No Fourth Wall episodes of Looney Tunes ("Duck Amuck"). In the preview Buford even calls his costume a daffodil, despite looking nothing like one. Could be coincidence. Probably isn't.
There's also a literal shout out in Bullseye! right in line with the one from The Secret of Success. In the middle of the musical number, the L.O.V.E.M.U.F.F.I.N singers belt out "YES! WE! CAN!"
The bird flying flying past the sun and then bursting into flames at the beginning of "Lawn Gnome Beach Party of Terror" might be a reference to the Family Guy episode "Brian, Portrait of a Dog".
"The Curse of Candace" begins with one of the greatest parodies of Twilight to date.
JARED: "I expect this from your kind, Michael—football players, I mean—but Kristen, I mean, we were both—moody outcasts! We...we loved each other!"
Later, after the movie ends, when Stacey and Candace exit the cinema hall, there is a poster revealing that the movie is called "Early Evening".
In "Got Game" 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.
In "Last Train to Bustville", 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".
In "Misperceived 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").
In "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 Dorathe Explorer (minus one "We did it").
The episode "Perry Lays an Egg" is full of references to Finding Nemo, specifically baby sea turtles, krill, and speaking whale language.
Among the ten thousand monsters gathered by Phineas and Ferb in "Excaliferb" is a Gargoyle resembling a green Goliath.
The title of "Monster from the ID" 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.
In "Gi-Ants", Doofenshmirtz gets the turkey from the Turkey-inator stuck on his head.
In "Tri-Stone Area", many of the characters come off this way, being cavepeople, but Buford in particular looks like he walked right off the set of The Flintstones.
Easily missed among the cave talk, Doofendung refers to prehistoric Perry as "Bunka da bunkakwunk." In the TV special, the Cat in the Hat claims that he's "a bunka in a bunkakwunk, in Eskimo."
In "Doof Dynasty", the training montage song "Way of the Platypus" contains multiple nods to Mulan, and has this lyric:
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.
The entire episode "Remains of the Platypus" 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.
For another absolutely epic Star Wars reference, we are given the opening credits of "Meapless in Seattle".
In "Delivery of Destiny," Paul the delivery guy shifts his truck to "turbo," causing it to jump down the street like KITT's turbo boosts in Knight Rider.
In "Agent Doof," Doof references The Duck Song ("And the duck says 'got any grapes?'") while on a coffee break with Agent P and the other agents. Needless to say, the duck is not amused.
The B-plot of "Let's Bounce" 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.