Near the ending, when Charlie says "holy smoke I reely pulled a Charlie Gordon that time" when he accidentally goes back to Miss Kinnian's class. It was a funny moment in what would otherwise be a a very solemn, depressing passage.
Charlie's progress reports after he learns about punctuation. Failing to understand what they mean and how to use them, he throws commas and random punctuation marks around haphazardly throughout his text.
"(Punctuation, is; fun!)"
The scene where he tries to figure out the Rorschach inkblot test near the beginning.