The most powerful was probably the end of Gets a Little Stranger. Wendy reveals her third ear, but Louis assures her that he still loves her. While saying this, he gives her a look that makes her feel confident that he means it.
Then there was the event that led up to this moment: Wendy Nogard is set to cross the Moral Event Horizon by "accidentally" dropping Mrs. Jewls' new baby out of the thirtieth story window, but on her way, being a mind reader, she hears the baby's thoughts of pure love and trust and undergoes a powerful Heel-Face Turn.
The end of the "Love and a Dead Rat" chapter in Falling Down, in which Dameon, whose crush on Mrs. Jewls was no secret, overcomes his teasing classmates and confesses his love to Mrs. Jewls despite knowing there is a Mr. Jewls. Mrs. Jewls tells Dameon she loves him too and it's okay even though she is married.
"Just because I love Mister Jewls, it doesn't mean I can't also love you. Love is different from most things." She picked up a piece of chalk. "If I gave my piece of chalk to someone, then I wouldn't have it anymore. But when I give my love to someone, I end up with more love than I started with. The more love you give away, the more you have left."
Benjamin Nushmutt spends most of the second book thinking that the other students only like him because they think his name is Mark Miller and worried that they'll turn on him when they learn the truth. When he finally does reveal his real name, they don't care and accept him wholeheartedly.
In the third book, Mrs. Zarves has a breakdown after a lifetime of no one ever noticing her existence finally gets to her. She tearfully leaves Wayside School, only to be stopped by the mysterious men in business suits who show up in each of the books. They assure her that her she matters, and that her students still need her.
The men in business suits are good at this. The chapter "Freedom" has Myron, who's always had a bit of a nervous problem, melt down when he compares his own stuck-in life to that of a bird outside his classroom window. As he sulks, the men arrive and offer him a choice: he can be safe, with all the little compromises and responsibility that comes with it... or he can be free. He thinks about it, and then chooses to be free. And nobody ever bothers him again.
He didn't work on the test. Instead, he pushed it aside and sat on the floor.