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", "I Scream, You Scream", "At the Car Wash", "That Sinking Feeling", "Phineas and Ferb's Quantum Boogaloo", "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")
 * Norm ("Hail Doofania!")
 * Baljeet ("Bowl-R-Ama Drama")
 * Unnamed dream Sergeant ("Phineas and Ferb Get Busted!")
 * Candace ("Phineas and Ferb Christmas Vacation!", "Suddenly Suzy")
 * Suzy ("Suddenly Suzy")
 * Kelly Osbourne ("Phineas and Ferb Musical Cliptastic Countdown Hosted by Kelly Osbourne")

"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", "The Chronicles of Meap", "What A Croc!", "Mission Marvel")
 * Doofenshmirtz ("Hail Doofania!")
 * Thaddeus "(Thaddeus and Thor")
 * Ferb ("Ladies and Gentlemen, Meet Max Modem!")
 * Irving ("What A Croc!")
 * Robot Phineas ("Where's Perry? (Part Two)")

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

 * Phineas (Main character to say it)
 * Irving ("Hide and Seek")
 * Ferb ("Fireside Girl Jamboree")
 * Stacy ("Put That Putter Away", "Bad Hair Day")
 * Candace ("Oh, There You Are, Perry", "Phineas and Ferb Hawaiian Vacation", "Misperceived Monotreme", "Escape from Phineas Tower", "Ask a Foolish Question", "Agent Doof", "Meapless in Seattle", "This Is Your Backstory", "For Your Ice Only", "Where's Pinky?", "Happy Birthday, Isabella")
 * Lawrence ("Comet Kermillian", "Out of Toon", "Tip of the Day", "Swiss Family Phineas", "Mommy Can You Hear Me?")
 * Isabella ("It's About Time!", "The Flying Fishmonger", "Cheer Up Candace", "The Lizard Whisperer", "Great Balls Of Water")
 * Major Monogram ("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", "Hail Doofania!", "Nerds of a Feather", "This Is Your Backstory", "Blackout!")
 * Linda ("Ladies and Gentlemen, Meet Max Modem!", "The Great Indoors", "A Real Boy", "Backyard Hodge Podge")
 * Jeremy ("Misperceived Monotreme")
 * Beckham ("My Fair Goalie")
 * Baljeet ("Bowl-R-Ama Drama", "That's the Spirit", "Monster from the Id", "Road to Danville")
 * Buford ("Cranius Maximus", "Primal Perry", "Mind Share")
 * Vivian ("Happy New Year!")

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.

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")

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")
 * Gretchen ("Monster from the Id")

Secretly, I'm very lonely

 * Bobbi Fabulous ("Dude, We're Getting the Band Back Together")
 * Norm ("Greece Lightning")
 * 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")

"My watermelon!"

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