In the episode "Going Batty" the students believe that Ms. Frizzle is a vampire and is going to turn them and their parents into vampires. As they try to get to their parents they discover that they're "too late" and their parents are hanging upside down with bat wings wrapped around them. Phoebe's response: "I love you anyway, Daddy. I'll love you forever."
In "The Holiday Special", Wanda replaces Arnold's toy soldier that she wrecked. Later, the episode's whole cast joins Arnold and his dad on what would have been a lonely train ride on the first night of Hanukkah.
Actually, it was Wanda's toy solder that Arnold accidentally got recycled. It gets turned into more toy solders made out of other recycled materials as well and donated to kids in need, and Wanda decided to join the class on the train instead of going to the ballet, which is what she'd been excited about for the whole episode and was the reason she was donating the toy solder.
In the book "Explores the Senses," Mrs. Frizzle expresses her pride at her daughter's teaching abilities, which have led both her (Valerie, not her mother) and the class to receive multiple awards. Also, this is one of several times in the books that we get to see how close Valerie really is to her various family members. She very pointedly makes time for her mother and even buys her a new outfit as a gift before meeting her for lunch.
Janet's reaction to Arnold taking off his helmet on Pluto. Even before he actually does it, Janet knows immediately what he's about to do and begs him not to. As mean as she is to him, she really does love him.
Also, the fact that Arnold was willing to risk death by hypothermia/suffocation to convince her to come home.