Stop-motion Cartoon

Stop-motion cartoons are an animated thing to make the thing walk and talk on its own.

Avaturd / CSiCarly

 * (Pumpkin Head Surgery)

TransBOREmores / Star Wars: the Groan Wars

 * (MAD News segment)

2012 Dalmatians / Grey's in Anime

 * (Trunk Joke)

Star Blecch / uGlee

 * (Caller ID)

Pirates of the Neverland: At Wit's End / Batman Family Feud

 * (MAD News segment)

Cliffordfield / Big Time Rushmore

 * (Learn to READ)

Fantastic Megan Fox / MAD vs. Wild

 * (Fantastic Megan Fox, MAD Security Cam segment) (Parody of Fantastic Mr. Fox and Megan Fox)

I Love You, Iron Man / Ben 10 Franklin

 * (MAD News segment, This Day in History segment)

Class of the Titans / Zeke and Lex Luthor

 * (MAD News segment, Waterproof Laptop)

S'UP / Mouse M.D.

 * (MAD News segment, Vampire Helper, MAD Security Cam segment)

Da Grinchy Code / Duck

 * (MAD News segment, Big B-- JACOB!!!) (Parody of Little Red Riding Hood and Jacob Black)

Snott Pilgrim vs. the Wonderful World of Disney / Malcolm in the Middle Earth

 * (MAD News segment, Papers Get Surrounded By Scissors)

Pokémon Park / WWER

 * (Fire Extinguisher Trapped)

So You Think You Can Train Your Dragon How to Dance / Yo Gagga Gagga!

 * (This Day in History segment)

The Straight A-Team / Gaming's Next Top Princess

 * (MAD Security Cam segment)

The Buzz Identity / Two and a Half Man

 * (Now Serving Number 2 and Mummy Thinks the Store is Closed)

Are You Karate Kidding Me? / The Fresh Prawn of Bel-Air

 * (Rooster Wake-up)

HOPS / Naru210

 * (Astronaut meets Swimmer)

Ko-Bee Movie / Law &amp; Ogre

 * (Dummies for Dummies) (Parody of For Dummies Books)

Pooh Grit / Not a Fan a Montana

 * (Potato Says About the French Fry, "She’s Definitely Got Work Done!")

The Social Netjerk / Smallville: Turn Off the Clark

 * (MAD Security Cam segment)

TwiGH School Musical / Avenger Time

 * (Fish Complaining About Worms)

ArTHOR / The Big Fang Theory

 * (Hand Disguised as a Sock Puppet)

Ribbitless / The Clawfice

 * (MAD Security Cam segment)

Force Code / Flammable

 * (This Day in History segment, Flammable) (Parody of Katy Perry's "Firework")

RiOa / Thomas the Unstoppable Tank Engine

 * (Tomato Dislikes Ketchup)

Super 80's / Captain America's Got Talent
Note: This is the first time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Kung Fu Blander / Destroy Bob the Builder Destroy

 * (Farmer Gets Milk for the Cow)

Pirates of the Pair of Tweens / Konan the Kardashian
Note: Second time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Fast Hive / Minute to Flynn It

 * (MAD Security Cam segment)

Cowboys &amp; Alien Force / ThunderLOLcats
Note: Third time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

TransBOREmores 3: Dark of the Blue Moon / The Walking Fred
Note: Fourth time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

X-Games: First Class / Criminal Minecraft

 * (MAD Security Cam segment)

Kitchen Nightmares Before Christmas / How I Met Your Mummy

 * (Kitchen Nightmares Before Christmas) (Parody of Kitchen Nightmares and Tim Burton's the Nightmare Before Christmas)

Dances with Wolverine: A Footloose Parody / Tater Tots &amp; Tiaras
Note: Fifth time Spy vs. Spy was done in stop-motion.
 * (SpongeWow! and Spy vs. Spy segment) (Parody of SpongeBob SquarePants and ShamWow!)

Moneyball Z / Green Care Bear

 * (Stunt Turkey)

Spy vs. Spy Kids / The Superhero Millionaire Matchmaker
Note: Sixth time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy and MAD Security Cam segments)

Captain American't / My Supernatural Sweet 16

 * (Mouse Doesn't Want Cheese) (Spoof on Applebee's)

FROST / Undercover Claus
Note: Seventh time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy and MAD Security Cam segments)

Twilight: Staking Dawn / Cookie Blue

 * (MAD Security Cam segment)

WWe Bought a ZOO / 2 Broke Powerpuff Girls
Note: Eighth time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

DolPhineas and Ferb Tale / VICTORious

 * (Pillsbury Dough Boy Conference) (Spoof on Pillsbury Dough Boy)

My Little War Horse / The Tonight Show with Jay Lion-O
Note: Ninth time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Al Pacino and the Chipmunks / That's What Super Friends Are For

 * (MAD Security Cam segment)

Real Veal / Celebrity Wife Swamp
Note: 10th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Garfield of Dreams / I Hate My Teenage Mutant Ninja Turtles

 * Robots of Humanco

The Adventures of TaunTaun / Everybody Loves Rayman
Note: 11th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Potions 11 / Moves Like Jabba

 * (MAD Security Cam segment)

Addition Impossible / New Gill
Note: 12th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

iChronicle / Hulk Smash
Note: 13th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

The Iron Giant Lady / Raising a New Hope
Note: 14th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Yawn Carter / Franklin & Crash
Note: 15th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Battleship vs. Titanic / Jurassic Parks and Recreation
Note: 16th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Betty White & the Huntsman / Ancient Greek MythBusters
Note: 17th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

I Am Lorax / Modern Family Circus
Note: 18th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

This Means War Machine / iCharlie
Note: 19th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

The Mixed Martial Artist / Aquaman vs. Wild
Note: 20th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

The Blunder Games / The Poop-seidon Adventure
Note: 21st time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Average-ers / Legend of Dora
Note: 22nd time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Men in Black to the Future / Pokémon of Interest
Note: 23rd time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Diary of a Wimpy Kid Icarus / Adjustment Burro
Note: 24th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Taking Nemo / Once Upon a Toon
Note: 25th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Outtagascar / F·I·E·N·D·S
Note: 26th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

The Amazing Spider-Minaj / Go, Dragon Ball, Go!
Note: 27th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

FrankenWinnie / ParaMorgan
Note: 28th time Spy vs. Spy was done in stop-motion.
 * (FrankenWinnie, Spy vs. Spy segment) (Parody of Frankenweenie and Winnie the Pooh)

Dark Knight at the Museum / Lemming Snicket's A Series of Unfortunate Video Game Deaths
Note: 29th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Total Recall Me Baby / The Asgardigans
Note: 30th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

The Bourne Leg-a-Turkey / PilGrimm
Note: 31st time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Here Comes the Doom / Brain Purge
Note: 32nd time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Fantastic Four Christmases / Red & White Collar
Note: 33rd time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Hip Hop Hobbit / The Monday Project
Note: 34th time Spy vs. Spy was done in stop-motion.
 * (MAD Security Cam and Spy vs. Spy)

The Perks of Being a Wallcrawler / Regular Shogun Warriors
Note: 35th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Twilight: Breaking Down / GOllum ON
Note: 36th time Spy vs. Spy was done in stop-motion.
 * (MAD Security Cam and Spy vs. Spy)

Life of Rhyme / Here Comes Yogi Boo Boo
Note: 37th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

James Bond: Reply All / Randy Savage: 9th Grade Wrestler
Note: 38th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

George Washington: Cherry Tree Chopper / Star Wars Earned Stripes
Note: 39th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Linkong / Rainbow Dash & Bernstein
Note: 40th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Pokémonsters, Inc. / Bane & Kate
Note: 41st time Spy vs. Spy was done in stop-motion.
 * (MAD Security Cam and Spy vs. Spy segment)

Wreck It Gandalph / The Big Bird Theory
Note: 42nd time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Les the Miz / The Lex Factor
Note: 43rd time Spy vs. Spy was done in stop-motion.
 * (MAD Security Cam and Spy vs. Spy segment)

Papa / 1600 Finn
Note: 44th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

G.I. E.I. Joe / Dog with a Captain's Log
Note: 45th time Spy vs. Spy was done in stop-motion.
 * (Not Karate Class, Book Club Actually and Spy vs. Spy segment)

"S" Cape from Planet Earth / The X-Mentalist
Note: 46th time Spy vs. Spy was done in stop-motion.
 * (Spy vs. Spy segment)

Trivia

 * In Season 2, some of the stop-motion cartoons are Spy vs. Spy segments.
 * Starting with Addition Impossible / New Gill, the stop-motion segments are currently Spy vs. Spy segments.