This movie may as well be Crowning Moment of Funny: The Movie for the sheer density of humor. But for specific examples:
* When Tails accidentally grabs Sara's breasts and gets called out by Knuckles for it.
-->'''Knuckles:''' TAILS! ''GET OFF!''
-->'''Tails:''' ''[Quickly leaps off Sara]'' [[MotorMouth I'msosorry...]]
-->'''Knuckles:''' [[LampshadeHanging I never thought you'd stoop that low!]]
* When Sara kisses Knuckles to motivate him, the formerly reluctant "mole" blushes and answers with a firm "Yes ma'am!"
* "MY HAT'S ON FIRE! HEEEELP!"
* "[[BigShutUp SHUT UP,]] [[MemeticMutation TAILS!]]"
* Sara, the President, Sonic, and Tails sleeping through Eggman's lecture. [[EvenTheDogIsAshamed Even Eggman's robots fall asleep.]]
--> '''Eggman: FINE! DON'T BLAME ME WHEN THIS HAPPENS!'''
--> ''Eggman pops his sphere representing Planet Freedom, [[http://www.youtube.com/watch?v=AgZWZDr4I8o and gets BAN'D by the sphere popping]].''
* Any interaction between Sara and Eggman, especially Sara's reaction to Eggman's plans to marry her.
* When he appears, Metal Robotnik causes an explosion that sends Sonic and Tails flying backwards. Sonic lands on his feet while Tails lands on his head.
* Sonic and Tails fighting Metal Robotnik by taunting it.
* Sonic and Metal Sonic's battle-
-->'''Sonic:''' You might know everything ''I'm'' going to do...but that's not going to help you, since I KNOW EVERYTHING ''YOU'RE'' GOING TO DO! '''''[[ChewingTheScenery STRRRRRAAAAANGE, ISN'T IT?!]]'''''
** Particularly, when Sonic falls [[GroinAttack crotch-first]] on the nose of Robotnik's ship and starts writhing in pain. At the same time, Metal Sonic crashes through the bottom of Robotnik's ship, [[PantyShot accidentally looks up Sara's dress]], and receives a kicking from her for it-
-->'''Eggman:''' Oh no, how is that you're still alive, Sonic?! ''[Sonic ignores him and carries on writhing in evident pain]'' Huh? What's wrong with you, what are you doing? ''[Looks behind him]''
-->'''Sara:''' ''[Holding her dress down as she repeatedly kicks Metal in the head]'' THAT'S BAD, [[RapidFireNo NO! NO! NO! NO! NO!]] ''[Metal continues staring up her skirt, [[MySensorsIndicateYouWantToTapThat its eyes glowing noticeably brighter]]]'' '''DON'T TOUCH THERE, YOU ''PERVERT!'''''
* Eggman taunting Sonic after the former fell into the latter's trap.
* The President's attempt to call Sonic, but instead finding Knuckles and the Owl.
* Eggman launches two missiles at Tails. The Hare Missile blows up the plane, but the Tortoise Missile... well, [[http://www.youtube.com/watch?v=4HtqqSZ4Zv8 it's just slow.]]
-->'''Eggman''': Oh no, [[NoodleIncident another]] design failure?
* Eggman's [[BrickJoke Tortoise Missile]] destroying his DNA data of Sonic.
* Sara falling on top of Knuckles, and then Tails crashing into them when Eggman is just about to recapture Sara- leading to the infamous bit mentioned above where he accidentally gropes her breasts.
* Sonic's [[RealMenWearPink 'favourite]] [[TotallyRadical clothes']]. By extension, just the fact that it looks like Metal Sonic is going to attack Old Man Owl when it confronts him at Sonic's house, but instead [[BaitAndSwitch gives him the clothes as a present]].
* "SHUT UP! '''HEED ME!'''"
*"AAAH! I'M AFRAID OF LIGHTNING!!"