Pretty much the entire scene after Spongebob and Patrick race from the Krusty Krab 2 to save Mr. Krabs, but special note goes to the introduction of The Patty Wagon. It's featured in all the trailers, but to hear Spongebob coolly run through it's "fast food" features and to have it blast out of the restaurant is still pretty damn epic. If anyone can make driving a burger equivalent of the weiner-mobile look cool, it's Spongebob.
Squidward becoming aware of Plankton's evil plan, and actually taking action in stopping it. Too bad Plankton activated the mind-control helmets before he can even do anything about it.
And too bad about the flaw in Squidward's plan. He shouldn't have threatened to expose Plankton before doing so.
SpongeBob giving an I Am What I Am speech before singing a rock and roll rendition of the Goofy Goober Theme Song, leading up to him using The Power of Rock to break everyone free from Plankton's mind-controlling helmets.