List of running gags

 are jokes or events that are seen throughout the series.

"What'cha doin'?"

 * Isabella (Main character to say it)
 * Phineas ("Flop Starz", "Run Away Runway", "Traffic Cam Caper", "I Scream, You Scream", "At the Car Wash", "That Sinking Feeling", "Phineas and Ferb's Quantum Boogaloo", "Nerdy Dancin'", "The Beak", "We Call it Maze", "Bullseye!")
 * Lawrence ("Greece Lightning", "Phineas and Ferb and the Temple of Juatchadoon")
 * Linda ("The Best Lazy Day Ever")
 * Buford ("Out of Toon", "Swiss Family Phineas", "Tri-Stone Area", "Blackout!", "La Candace-Cabra")
 * Major Monogram ("Phineas and Ferb Musical Cliptastic Countdown")
 * Norm ("Hail Doofania!")
 * Baljeet ("Bowl-R-Ama Drama")
 * Unnamed dream Sergeant ("Phineas and Ferb Get Busted!")
 * Candace ("Phineas and Ferb Christmas Vacation!", "Suddenly Suzy", "Monster from the Id")
 * Suzy ("Suddenly Suzy")
 * Kelly Osbourne ("Phineas and Ferb Musical Cliptastic Countdown Hosted by Kelly Osbourne")
 * Jeremy Johnson ("Return Policy")

"I know what we're gonna do today!"

 * Phineas (main character to say it)
 * Candace ("Run Away Runway", "Phineas and Ferb Get Busted!", "Finding Mary McGuffin", "Phineas and Ferb-Busters!", "The Chronicles of Meap", "Phineas' Birthday Clip-O-Rama!", "What A Croc!", "Meapless in Seattle", "Phineas and Ferb: Mission Marvel")
 * Doofenshmirtz ("Hail Doofania!")
 * Thaddeus "(Thaddeus and Thor")
 * Baljeet "(Not Phineas and Ferb")
 * Ferb ("Ladies and Gentlemen, Meet Max Modem!")
 * Irving ("What A Croc!")
 * Robot Phineas ("Where's Perry? (Part Two)")
 * Mr. Macabre ("Terrifying Tri-State Trilogy of Terror")

"Where's Perry?" and "Oh, there you are, Perry"

 * Phineas (Main character to say it)
 * Irving ("Hide and Seek", "Just Desserts", "Phineas and Ferb: Mission Marvel")
 * Ferb ("Fireside Girl Jamboree", "Lost in Danville")
 * Stacy ("Put That Putter Away", "Bad Hair Day")
 * Candace ("Mom's Birthday", "Oh, There You Are, Perry", "Unfair Science Fair Redux (Another Story)", "Phineas and Ferb Hawaiian Vacation", "Ask a Foolish Question", "Misperceived Monotreme", "Escape from Phineas Tower", "Tour de Ferb", "Ask a Foolish Question", "Agent Doof", "Meapless in Seattle", "This Is Your Backstory", "For Your Ice Only", "Where's Pinky?", "Happy Birthday, Isabella", "Just Our Luck", "Live and Let Drive")
 * Lawrence ("Comet Kermillian", "Out of Toon", "Tip of the Day", "Swiss Family Phineas", "Mommy Can You Hear Me?", "Love at First Byte")
 * Isabella ("It's About Time!", "The Flying Fishmonger", "Cheer Up Candace", "The Lizard Whisperer", "Great Balls Of Water", "The Return of the Rogue Rabbit")
 * Major Monogram ("Lights, Candace, Action!", "The Magnificent Few", "Toy to the World", "Dude, We're Getting the Band Back Together", "Tree to Get Ready", "Phineas and Ferb-Busters!")
 * Unnamed hotel manager ("Phineas and Ferb Hawaiian Vacation")
 * Chaka Khan ("Phineas and Ferb Summer Belongs to You!")
 * Doofenshmirtz ("Tree to Get Ready", "Oil on Candace", "Hail Doofania!", "Swiss Family Phineas", "Nerds of a Feather", "This Is Your Backstory", "Blackout!")
 * Linda ("Ready For The Bettys", "Ladies and Gentlemen, Meet Max Modem!", "The Great Indoors", "A Real Boy", "Backyard Hodge Podge", "Imperfect Storm")
 * Beckham ("My Fair Goalie")
 * Baljeet ("Bowl-R-Ama Drama", "Swiss Family Phineas", "That's the Spirit", "Monster from the Id", "Road to Danville", "Face Your Fear", "Return Policy")
 * Buford ("Cranius Maximus", "Primal Perry", "Mind Share", "One Good Turn", "Cheers for Fears")
 * Vivian ("Happy New Year!")
 * Whiplash ("Phineas and Ferb: Mission Marvel")
 * Reginald Fletcher ("Father's Day")

Ferb gets cut off mid-sentence

 * "Vanessassary Roughness" (We learn Ferb is short for something)
 * "Get That Bigfoot Outa My Face!"
 * "Ready for the Bettys" (Repeatedly)
 * "Undercover Carl"
 * "We Call it Maze"
 * "Nerds of a Feather"
 * "My Fair Goalie"
 * "Disney's Phineas and Ferb: The Best LIVE Tour Ever!"

The bird that runs into Phineas and Ferb's invention
Often, the bird strike occurs after a slow camera pan up an object as the music reaches a crescendo.
 * "Rollercoaster" and "Rollercoaster: The Musical!" - A bird hits the rollercoaster track and falls to the ground.
 * "Candace Loses Her Head" - A bird hits the canvas rendition of Mount Rushmore. Later, when the real monument is revealed, we hear the sound of a bird hitting the monument.
 * "Lawn Gnome Beach Party of Terror" - A bird flies by the sun and burns into flames.
 * "Out to Launch" - A bird hits the rocket during the countdown.
 * "Thaddeus and Thor" - Doofenshmirtz's practice kick disrupts some birds in a tree. His game kick hits Phineas' and Ferb's fort at the appropriate point during the camera pan.
 * "Picture This" - Ferb opens a trapdoor in the huge skateboarding half-pipe as a bird approaches.
 * "The Doof Side of the Moon" - Two birds run into building at the same time as the moon starts to move along with the building.
 * "Split Personality" - A bird runs into Danville's high-dive tower.
 * "Phineas' Birthday Clip-O-Rama!" - While running with the DVD, Candace is "attacked" by birds knocked out of the sky by the flying pipe piece.
 * "Candace Disconnected" - Candace flies through a swarm of birds while flying on the Pick-Em-Up-Inator.
 * "Meatloaf Surprise" - During Phineas' speech the bird can be seen flying towards the fan but being blown away.
 * "My Fair Goalie" - Not Phineas and Ferb's invention, but in the informational video on Football X-7, a bird hits Professor Ross E. Forp's original prototype Football X-7 stadium.
 * "Doof Dynasty" - birds run into a giant terracotta warrior.
 * "Excaliferb" - a bird flies over the chimney and bursts into flames.
 * "Gi-Ants" - Instead of a bird, a housefly runs in Phineas' "invetsors' version" of the giant Ant Farm.
 * "Imperfect Storm" - A bird is blown away by the wind amplification device. Another bird gets into Ferb's pterodactyl kite, but Ferb sets it free.

Things that have fallen out of the sky

 * Ice cream (a cone in "Raging Bully" and a quart in "Swiss Family Phineas ")
 * Miniature golf course ("Put That Putter Away")
 * Steaks ("Comet Kermillian")
 * Rabbits, and later a van ("Leave the Busting to Us!")
 * Pizzazium Infantinite as the perfect lantern ("Vanessassary Roughness")
 * A giant present ("Phineas and Ferb Christmas Vacation!")
 * A cat ("saved" by Doofenshmirtz) ("Voyage to the Bottom of Buford")
 * Phineas and Ferb's replica of Niagara Falls ("Suddenly Suzy")
 * A battery cart ("Rollercoaster: The Musical!")
 * Heinz Doofenshmirtz and a Dodo Bird ("Last Train to Bustville")
 * Phineas and Ferb's ice scorpion ("Candace's Big Day")
 * Waffles ("Phineas and Ferb: Mission Marvel")

Out, Peace!

 * Candace (Main character to say it)
 * Unknown guy ("Unfair Science Fair Redux (Another Story)")
 * Ferb's Scottish cousin ("Invasion of the Ferb Snatchers")
 * Narrator guy ("The Beak")
 * Melanie ("She's the Mayor")
 * Single guy ("Phineas and Ferb Hawaiian Vacation")
 * Doofenshmirtz ("Nerds of a Feather", Disney XD premiere of "Phineas and Ferb: Mission Marvel", "DOOF RAPS ON RAP" episode of Doofenshmirtz's Daily Dirt)
 * Gretchen ("Monster from the Id")

Secretly, I'm very lonely

 * Bobbi Fabulous ("Dude, We're Getting the Band Back Together")
 * Norm ("Greece Lightning", "Where's My Perry?")
 * Doofenshmirtz ("Let's Bounce")

Mistaking Doofenshmirtz for a pharmacist

 * Mall patrons ("Run Away Runway")
 * Candace ("The Ballad of Badbeard")
 * Buford ("Brain Drain")
 * Baljeet ("Brain Drain")
 * Lawrence ("Road Trip", "Bullseye!")
 * Phineas (Phineas and Ferb The Movie: Across the 2nd Dimension)
 * Robbie Wyckoff (Phineas and Ferb: Across the 2nd Dimension (video game))
 * Johnny ("Skiddley Whiffers)
 * Archaeologist ("Lotsa Latkes")
 * Judge ("What'd I Miss?")
 * Norm ("Happy New Year!")
 * Gretchen ("Bee Story")
 * Liam McCracken ("Primal Perry")
 * Stacy ("Happy Birthday, Isabella")
 * Gordon Gutsofanemu ("Phineas and Ferb: Mission Marvel")
 * Episode title ("Night of the Living Pharmacists")

"My watermelon!"

 * Phineas and Ferb The Movie: Across the 2nd Dimension
 * "The Mom Attractor"
 * "When Worlds Collide"
 * "Blackout!"
 * "Phineas and Ferb: Star Wars"