SpongeBob: No, that we're just...kids. A couple of kids in way over their heads. We were doomed from the start. I mean look at us. We didn't even come close to the crown. We let everybody down...we failed...
Spongebob had been around for five years when this movie came out. He was a legend. Making kids and adults alike smile. When he gets to the trench he just gives up. The Spongebob we all know and love, who had entertained generations with his chocolate selling antics and his fry cooking expertise just collapses, and can't go on.
After Plankton walks into the Krusty Krab and steals the formula, there's a brief shot of frozen Mr. Krabs shedding a single tear that immediately freezes and hits the ground.
Spongebob and Patrick's reactions after learning that all their friends back home have become slaves of Plankton.
Wilco's song for this movie, Just a Kid. Remember, this is chronologically the end of the series. It really hits home to fans who grew up with Spongebob during Seasons 1-3, and it also speaks to anyone who's moving on in life whether it be graduating from high school/college, moving out, getting a new job etc. The song even says "Someone, anyone, everybody has to grow up".
Meta example: old-time Spongebob fans may have a hard time watching considering this is technically the end of the series, and was meant to be a Grand Finale, and may see the ending as the point where Spongebob (the "good" Spongebob, at least) ended forever.